Config
Job: expected-2
align:
mafft:
- --6merpair
- --keeplength
- --addfragments
resources:
mem_mb: 8000
runtime: 10
threads: 4
all:
threads_max: 64
update_default_resources: null
beast:
beast:
- -beagle_SSE
- -seed 98202873
dynamic:
- ePopSize=0.3
- Date.dateFormat=yyyy/MM/dd
- Date.delimiter=_
- mutationRate=1.0
- mcmc.chainLength=10000
- treelog.logEvery=1000
- tracelog.logEvery=1000
resources:
mem_mb: 16000
runtimtime: 1200
threads: 6
data:
- /Users/smutch/work/mdap/collabs/2022/duchene/mccoy/tests/expected/runs/run_1/data/combined/expected-1.fasta
- /Users/smutch/work/mdap/collabs/2022/duchene/mccoy/tests/data2.fasta
id: expected-2
inherit: tests/expected/runs/run_1
project_id: expected
project_path: /Users/smutch/work/mdap/collabs/2022/duchene/mccoy/tests/expected
run_id: 2
run_name: run_2
tree:
iqtree2:
- -nt AUTO
- -m HKY+G
- -bb 1000
- -seed 847202098
resources:
mem_mb: 16000
runtime: 20
threads: 10
Alignment
General Characteristics ======================= 138 Number of taxa 1734 Alignment length 81 Parsimony informative sites 190 Variable sites 1544 Constant sites Character Frequencies ===================== Y 1 W 1 T 57893 R 1 M 2 G 52082 C 47452 A 81527 - 333
GC content: 0.4165
Relative composition variability: 0.0035
Pairwise Identity
The proportion of colums that agree between pairs in the alignment. See PhyKIT docs.
mean: 0.9926 median: 0.9925 25th percentile: 0.9908 75th percentile: 0.9948 minimum: 0.9804 maximum: 1.0 standard deviation: 0.0031 variance: 0.0
Maximum Likelihood Tree
IQ-TREE 2.1.2 COVID-edition built Mar 30 2021
Input file name: results/aligned/expected-2.fasta
Type of analysis: tree reconstruction + ultrafast bootstrap (1000 replicates)
Random seed number: 847202098
REFERENCES
----------
To cite IQ-TREE please use:
Bui Quang Minh, Heiko A. Schmidt, Olga Chernomor, Dominik Schrempf,
Michael D. Woodhams, Arndt von Haeseler, and Robert Lanfear (2020)
IQ-TREE 2: New models and efficient methods for phylogenetic inference
in the genomic era. Mol. Biol. Evol., in press.
https://doi.org/10.1093/molbev/msaa015
Since you used ultrafast bootstrap (UFBoot) please also cite:
Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler, Bui Quang Minh,
and Le Sy Vinh (2018) UFBoot2: Improving the ultrafast bootstrap
approximation. Mol. Biol. Evol., 35:518–522.
https://doi.org/10.1093/molbev/msx281
SEQUENCE ALIGNMENT
------------------
Input data: 138 sequences with 1734 nucleotide sites
Number of constant sites: 1547 (= 89.2157% of all sites)
Number of invariant (constant or ambiguous constant) sites: 1547 (= 89.2157% of all sites)
Number of parsimony informative sites: 81
Number of distinct site patterns: 181
SUBSTITUTION PROCESS
--------------------
Model of substitution: HKY+F+G4
Rate parameter R:
A-C: 1.0000
A-G: 10.1646
A-T: 1.0000
C-G: 1.0000
C-T: 10.1646
G-T: 1.0000
State frequencies: (empirical counts from alignment)
pi(A) = 0.3412
pi(C) = 0.1986
pi(G) = 0.218
pi(T) = 0.2423
Rate matrix Q:
A -0.8905 0.06658 0.7427 0.08122
C 0.1144 -1.013 0.07307 0.8256
G 1.163 0.06658 -1.31 0.08122
T 0.1144 0.6768 0.07307 -0.8642
Model of rate heterogeneity: Gamma with 4 categories
Gamma shape alpha: 0.4377
Category Relative_rate Proportion
1 0.02251 0.25
2 0.2093 0.25
3 0.7691 0.25
4 2.999 0.25
Relative rates are computed as MEAN of the portion of the Gamma distribution falling in the category.
MAXIMUM LIKELIHOOD TREE
-----------------------
Log-likelihood of the tree: -4072.2741 (s.e. 112.0757)
Unconstrained log-likelihood (without tree): -3759.5081
Number of free parameters (#branches + #model parameters): 266
Akaike information criterion (AIC) score: 8676.5482
Corrected Akaike information criterion (AICc) score: 8773.3744
Bayesian information criterion (BIC) score: 10128.4257
Total tree length (sum of branch lengths): 0.1257
Sum of internal branch lengths: 0.0326 (25.9065% of tree length)
WARNING: 85 near-zero internal branches (<0.0006) should be treated with caution
Such branches are denoted by '**' in the figure below
NOTE: Tree is UNROOTED although outgroup taxon 'CY068113_A_California_VRDL374_2009_2009/04/25' is drawn at root
Numbers in parentheses are ultrafast bootstrap support (%)
+-----CY068113_A_California_VRDL374_2009_2009/04/25
|
| +**CY068838_A_California_VRDL384_2009_2009/04/25
| +---------------| (100)
| | +--CY068625_A_California_VRDL338_2009_2009/05/18
| +-----| (97)
| | | +**CY072198_A_California_VRDL385_2009_2009/04/26
| | | +**| (16)
| | | | | +--CY068846_A_California_VRDL387_2009_2009/04/27
| | | | | +-----| (97)
| | | | | | | +**CY068750_A_California_VRDL201_2009_2009/04/29
| | | | | | +**| (60)
| | | | | | +**CY068241_A_California_VRDL212_2009_2009/04/29
| | | | | +**| (7)
| | | | | | | +**CY068633_A_California_VRDL394_2009_2009/04/28
| | | | | | | +**| (24)
| | | | | | | | +**CY068734_A_California_VRDL198_2009_2009/04/28
| | | | | | +**| (26)
| | | | | | +**CY068481_A_California_VRDL310_2009_2009/04/30
| | | | | +**| (20)
| | | | | | | +**CY068153_A_California_VRDL161_2009_2009/04/28
| | | | | | +**| (21)
| | | | | | +**CY068185_A_California_VRDL168_2009_2009/04/29
| | | | | +**| (14)
| | | | | | | +**CY068233_A_California_VRDL211_2009_2009/04/28
| | | | | | +-----| (98)
| | | | | | +**CY068537_A_California_VRDL321_2009_2009/05/04
| | | | | +**| (11)
| | | | | | | +--------CY068209_A_California_VRDL172_2009_2009/04/28
| | | | | | +**| (13)
| | | | | | +-----CY068774_A_California_VRDL205_2009_2009/04/29
| | | | +**| (14)
| | | | +**CY068710_A_California_VRDL185_2009_2009/04/29
| | | +**| (20)
| | | | +**CY068814_A_California_VRDL269_2009_2009/04/30
| | | +--| (96)
| | | | +-----CY068305_A_California_VRDL250_2009_2009/04/29
| | | +**| (24)
| | | | | +**CY068878_A_California_VRDL393_2009_2009/04/29
| | | | +-----| (99)
| | | | +**CY068385_A_California_VRDL271_2009_2009/04/30
| | | +**| (19)
| | | | | +--CY064879_A_California_VRDL147_2009_2009/04/28
| | | | +**| (16)
| | | | | +**CY068678_A_California_VRDL178_2009_2009/04/28
| | | | | +**| (75)
| | | | | | +**CY068257_A_California_VRDL230_2009_2009/04/29
| | | | | +**| (63)
| | | | | | +**CY068790_A_California_VRDL208_2009_2009/04/29
| | | | +--| (96)
| | | | +**CY092361_A_California_VRDL242_2009_2009/04/29
| | | +--| (89)
| | | | +--CY068289_A_California_VRDL247_2009_2009/04/29
| | +--| (92)
| | +-----CY067205_A_California_VRDL291_2009_2009/05/01
| +--| (91)
| | +---------------CY068758_A_California_VRDL203_2009_2009/04/28
| +--------| (99)
| | | +**CY064815_A_California_VRDL136_2009_2009/04/26
| | | +**| (87)
| | | | +**CY068161_A_California_VRDL164_2009_2009/04/28
| | | +------------------| (100)
| | | | +--CY067221_A_California_VRDL302_2009_2009/04/28
| | | +**| (65)
| | | | | +-----CY068145_A_California_VRDL160_2009_2009/04/28
| | | | +--| (92)
| | | | +-----CY068201_A_California_VRDL170_2009_2009/04/28
| | | +--| (94)
| | | | +--CY067937_A_California_VRDL286_2009_2009/04/30
| | | +**| (31)
| | | | | +**CY068249_A_California_VRDL216_2009_2009/04/28
| | | | +--| (98)
| | | | +**CY068473_A_California_VRDL309_2009_2009/05/02
| | | +**| (15)
| | | | | +**CY068694_A_California_VRDL183_2009_2009/04/27
| | | | | +--| (96)
| | | | | | +**CY068425_A_California_VRDL279_2009_2009/04/30
| | | | +**| (13)
| | | | +---------------CY068593_A_California_VRDL333_2009_2009/05/06
| | | +**| (9)
| | | | | +**CY064847_A_California_VRDL143_2009_2009/04/27
| | | | | +------------| (100)
| | | | | | +-----CY092329_A_California_VRDL182_2009_2009/04/28
| | | | | +**| (15)
| | | | | | +---------------CY068441_A_California_VRDL293_2009_2009/04/30
| | | | +**| (15)
| | | | +------------CY092353_A_California_VRDL197_2009_2009/04/29
| | | +**| (8)
| | | | | +**CY072206_A_California_VRDL386_2009_2009/04/26
| | | | | +--| (78)
| | | | | | +--------CY068273_A_California_VRDL233_2009_2009/04/29
| | | | | +**| (25)
| | | | | | | +**CY068798_A_California_VRDL210_2009_2009/04/28
| | | | | | +--------| (99)
| | | | | | +--CY068369_A_California_VRDL266_2009_2009/04/30
| | | | +**| (14)
| | | | +**CY064887_A_California_VRDL158_2009_2009/04/27
| | | +**| (18)
| | | | | +**CY068830_A_California_VRDL383_2009_2009/04/26
| | | | | +--| (99)
| | | | | | +--CY067985_A_California_VRDL342_2009_2009/05/20
| | | | | +**| (65)
| | | | | | +-----CY067253_A_California_VRDL316_2009_2009/05/04
| | | | | +--| (93)
| | | | | | | +**CY068465_A_California_VRDL308_2009_2009/04/29
| | | | | | +-----| (100)
| | | | | | +**CY068545_A_California_VRDL322_2009_2009/05/04
| | | | +**| (16)
| | | | | +-----CY068726_A_California_VRDL196_2009_2009/04/29
| | | | +**| (16)
| | | | | +**CY072190_A_California_VRDL347_2009_2009/05/23
| | | | +--| (97)
| | | | +**CY068025_A_California_VRDL351_2009_2009/05/23
| | | +**| (44)
| | | | | +**CY064855_A_California_VRDL144_2009_2009/04/27
| | | | +--| (98)
| | | | | +**CY068862_A_California_VRDL391_2009_2009/04/28
| | | | +**| (68)
| | | | +**CY067229_A_California_VRDL304_2009_2009/05/07
| | | +--| (91)
| | | | | +**CY064823_A_California_VRDL138_2009_2009/04/27
| | | | | +**| (47)
| | | | | | | +**CY068377_A_California_VRDL268_2009_2009/04/30
| | | | | | +**| (31)
| | | | | | +**CY068417_A_California_VRDL278_2009_2009/04/30
| | | | | +**| (63)
| | | | | | +**CY068401_A_California_VRDL274_2009_2009/04/30
| | | | +------------| (99)
| | | | +--CY066519_A_California_VRDL156_2009_2009/04/28
| | | +--| (78)
| | | | +----------------------CY068609_A_California_VRDL335_2009_2009/05/03
| | | +**| (34)
| | | | +---------------------------------------CY068313_A_California_VRDL253_2009_2009/04/30
| | | +**| (9)
| | | | | +--CY068177_A_California_VRDL166_2009_2009/04/28
| | | | | +-----| (98)
| | | | | | +**CY068193_A_California_VRDL169_2009_2009/04/28
| | | | +**| (10)
| | | | +---------------CY068449_A_California_VRDL294_2009_2009/04/30
| | +**| (24)
| | | +-----------------------------CY068782_A_California_VRDL207_2009_2009/04/27
| | | +**| (88)
| | | | +--------CY067929_A_California_VRDL177_2009_2009/04/28
| | +**| (29)
| | +---------------CY068097_A_California_VRDL368_2009_2009/04/27
| +-----| (97)
| | +**CY092369_A_California_VRDL255_2009_2009/04/29
| +**| (21)
| | +------------CY067953_A_California_VRDL288_2009_2009/04/30
| +**| (12)
| | +--CY068121_A_California_VRDL375_2009_2009/04/27
| +**| (4)
| | | +---------------CY068321_A_California_VRDL259_2009_2009/04/29
| | | +**| (48)
| | | | +---------------CY068617_A_California_VRDL336_2009_2009/05/05
| | +**| (16)
| | +--CY068433_A_California_VRDL285_2009_2009/04/30
| +**| (5)
| | | +**CY067921_A_California_VRDL176_2009_2009/04/27
| | | +**| (89)
| | | | +**CY068041_A_California_VRDL354_2009_2009/05/26
| | | +--| (90)
| | | | | +**CY068822_A_California_VRDL381_2009_2009/04/27
| | | | | +**| (81)
| | | | | | +**CY067237_A_California_VRDL307_2009_2009/05/02
| | | | +--| (99)
| | | | +--CY068561_A_California_VRDL327_2009_2009/05/11
| | | +--| (92)
| | | | +-----CY068065_A_California_VRDL360_2009_2009/06/03
| | +**| (8)
| | | +**CY068033_A_California_VRDL352_2009_2009/05/11
| | | +-----| (97)
| | | | +**CY068049_A_California_VRDL355_2009_2009/05/11
| | +**| (35)
| | | +**CY068009_A_California_VRDL345_2009_2009/05/26
| | +------------| (100)
| | +**CY068017_A_California_VRDL349_2009_2009/05/26
| +**| (19)
| | | +-----CY068129_A_California_VRDL396_2009_2009/04/28
| | +**| (19)
| | +--CY068585_A_California_VRDL332_2009_2009/05/11
| +--| (87)
| | | +--CY068854_A_California_VRDL390_2009_2009/04/26
| | | +**| (42)
| | | | +-----CY068686_A_California_VRDL181_2009_2009/04/28
| | | +**| (21)
| | | | | +**CY068457_A_California_VRDL305_2009_2009/05/01
| | | | +--| (99)
| | | | +**CY067245_A_California_VRDL314_2009_2009/05/01
| | | +**| (3)
| | | | | +**CY064863_A_California_VRDL145_2009_2009/04/27
| | | | | +**| (20)
| | | | | | +**CY068105_A_California_VRDL373_2009_2009/04/27
| | | | | +**| (2)
| | | | | | | +**CY068169_A_California_VRDL165_2009_2009/04/29
| | | | | | +**| (41)
| | | | | | +**CY068329_A_California_VRDL260_2009_2009/05/01
| | | | | +**| (45)
| | | | | | | +**CY068297_A_California_VRDL248_2009_2009/04/27
| | | | | | +**| (17)
| | | | | | +**CY068870_A_California_VRDL392_2009_2009/04/28
| | | | | +--------| (99)
| | | | | | | +--CY068497_A_California_VRDL313_2009_2009/05/01
| | | | | | +**| (7)
| | | | | | +--CY068505_A_California_VRDL315_2009_2009/05/01
| | | | | +**| (61)
| | | | | | | +**CY068702_A_California_VRDL184_2009_2009/04/28
| | | | | | +--| (99)
| | | | | | +**CY068529_A_California_VRDL319_2009_2009/05/06
| | | | | +**| (19)
| | | | | | | +**CY068742_A_California_VRDL199_2009_2009/04/28
| | | | | | | +**| (10)
| | | | | | | | +**CY068569_A_California_VRDL329_2009_2009/05/09
| | | | | | +**| (50)
| | | | | | +**CY068393_A_California_VRDL272_2009_2009/04/30
| | | | | +--| (95)
| | | | | | | +**CY067977_A_California_VRDL340_2009_2009/05/04
| | | | | | +**| (70)
| | | | | | +**CY068513_A_California_VRDL317_2009_2009/05/06
| | | | | +**| (34)
| | | | | | +--CY068353_A_California_VRDL263_2009_2009/04/30
| | | | | +**| (21)
| | | | | | +**CY068137_A_California_VRDL159_2009_2009/04/28
| | | | +**| (9)
| | | | +**CY068577_A_California_VRDL331_2009_2009/05/11
| | | +**| (32)
| | | | | +**CY068217_A_California_VRDL173_2009_2009/04/28
| | | | +**| (34)
| | | | +**CY068806_A_California_VRDL246_2009_2009/04/29
| | | +--| (91)
| | | | +--CY067213_A_California_VRDL296_2009_2009/04/30
| | +--| (87)
| | +--------CY067969_A_California_VRDL339_2009_2009/05/04
| +**| (18)
| | | +--------CY092377_A_California_VRDL257_2009_2009/05/01
| | +**| (25)
| | +--CY068001_A_California_VRDL344_2009_2009/05/19
| +**| (14)
| | +**CY068409_A_California_VRDL277_2009_2009/04/30
+**| (20)
| | +--------CY068766_A_California_VRDL204_2009_2009/04/28
| | +**| (24)
| | | +--CY067993_A_California_VRDL343_2009_2009/05/11
| | +**| (10)
| | | +**CY067197_A_California_VRDL241_2009_2009/04/29
| +**| (14)
| | +**CY068718_A_California_VRDL187_2009_2009/04/28
| | +**| (26)
| | | +**CY068265_A_California_VRDL231_2009_2009/04/30
| | +**| (15)
| | | +--CY089540_A_California_VRDL359_2009_2009/06/08
| +**| (9)
| | +--CY068281_A_California_VRDL243_2009_2009/04/29
| +**| (12)
| | +-----CY068521_A_California_VRDL318_2009_2009/05/06
| +--| (92)
| | +**CY067961_A_California_VRDL328_2009_2009/05/09
| +-----| (97)
| +**CY070919_A_California_VRDL330_2009_2009/05/09
|
| +**CY067945_A_California_VRDL287_2009_2009/05/04
+--| (99)
+**CY068057_A_California_VRDL357_2009_2009/06/05
Tree in newick format:
(CY068113_A_California_VRDL374_2009_2009/04/25:0.0011575643,((((((((((((((CY068838_A_California_VRDL384_2009_2009/04/25:0.0000010000,CY068625_A_California_VRDL338_2009_2009/05/18:0.0005787291)100:0.0029221677,(((((((CY072198_A_California_VRDL385_2009_2009/04/26:0.0000010000,((((((CY068846_A_California_VRDL387_2009_2009/04/27:0.0005797179,(CY068750_A_California_VRDL201_2009_2009/04/29:0.0000010000,CY068241_A_California_VRDL212_2009_2009/04/29:0.0000010000)60:0.0000010000)97:0.0011601151,((CY068633_A_California_VRDL394_2009_2009/04/28:0.0000010000,CY068734_A_California_VRDL198_2009_2009/04/28:0.0000010000)24:0.0000010000,CY068481_A_California_VRDL310_2009_2009/04/30:0.0000010000)26:0.0000010000)7:0.0000010000,(CY068153_A_California_VRDL161_2009_2009/04/28:0.0000010000,CY068185_A_California_VRDL168_2009_2009/04/29:0.0000010000)21:0.0000010000)20:0.0000010000,(CY068233_A_California_VRDL211_2009_2009/04/28:0.0000010000,CY068537_A_California_VRDL321_2009_2009/05/04:0.0000010000)98:0.0011580626)14:0.0000010000,(CY068209_A_California_VRDL172_2009_2009/04/28:0.0017411030,CY068774_A_California_VRDL205_2009_2009/04/29:0.0011594823)13:0.0000010000)11:0.0000010000,CY068710_A_California_VRDL185_2009_2009/04/29:0.0000010000)14:0.0000010000)16:0.0000010000,CY068814_A_California_VRDL269_2009_2009/04/30:0.0000010000)20:0.0000010000,CY068305_A_California_VRDL250_2009_2009/04/29:0.0011643843)96:0.0005784596,(CY068878_A_California_VRDL393_2009_2009/04/29:0.0000010000,CY068385_A_California_VRDL271_2009_2009/04/30:0.0000010000)99:0.0011598442)24:0.0000010000,(CY064879_A_California_VRDL147_2009_2009/04/28:0.0005789401,(((CY068678_A_California_VRDL178_2009_2009/04/28:0.0000010000,CY068257_A_California_VRDL230_2009_2009/04/29:0.0000010000)75:0.0000010000,CY068790_A_California_VRDL208_2009_2009/04/29:0.0000010000)63:0.0000010000,CY092361_A_California_VRDL242_2009_2009/04/29:0.0000010000)96:0.0005782157)16:0.0000010000)19:0.0000010000,CY068289_A_California_VRDL247_2009_2009/04/29:0.0005789840)89:0.0005783740,CY067205_A_California_VRDL291_2009_2009/05/01:0.0011620821)92:0.0005771451)97:0.0011642056,CY068758_A_California_VRDL203_2009_2009/04/28:0.0029140986)91:0.0005807590,(((((((((((((((CY064815_A_California_VRDL136_2009_2009/04/26:0.0000010000,CY068161_A_California_VRDL164_2009_2009/04/28:0.0000010000)87:0.0000010000,CY067221_A_California_VRDL302_2009_2009/04/28:0.0005829943)100:0.0034954704,(CY068145_A_California_VRDL160_2009_2009/04/28:0.0011589414,CY068201_A_California_VRDL170_2009_2009/04/28:0.0011631444)92:0.0005771451)65:0.0000010000,CY067937_A_California_VRDL286_2009_2009/04/30:0.0005816489)94:0.0005788645,(CY068249_A_California_VRDL216_2009_2009/04/28:0.0000010000,CY068473_A_California_VRDL309_2009_2009/05/02:0.0000010000)98:0.0005798900)31:0.0000010000,((CY068694_A_California_VRDL183_2009_2009/04/27:0.0000010000,CY068425_A_California_VRDL279_2009_2009/04/30:0.0000010000)96:0.0005786539,CY068593_A_California_VRDL333_2009_2009/05/06:0.0029148694)13:0.0000010000)15:0.0000010000,(((CY064847_A_California_VRDL143_2009_2009/04/27:0.0000010000,CY092329_A_California_VRDL182_2009_2009/04/28:0.0011609389)100:0.0023284475,CY068441_A_California_VRDL293_2009_2009/04/30:0.0029072453)15:0.0000010000,CY092353_A_California_VRDL197_2009_2009/04/29:0.0023242763)15:0.0000010000)9:0.0000010000,(((CY072206_A_California_VRDL386_2009_2009/04/26:0.0000010000,CY068273_A_California_VRDL233_2009_2009/04/29:0.0017404570)78:0.0005792918,(CY068798_A_California_VRDL210_2009_2009/04/28:0.0000010000,CY068369_A_California_VRDL266_2009_2009/04/30:0.0005818888)99:0.0017390489)25:0.0000010000,CY064887_A_California_VRDL158_2009_2009/04/27:0.0000010000)14:0.0000010000)8:0.0000010000,((((CY068830_A_California_VRDL383_2009_2009/04/26:0.0000010000,CY067985_A_California_VRDL342_2009_2009/05/20:0.0005803658)99:0.0005792159,CY067253_A_California_VRDL316_2009_2009/05/04:0.0011581926)65:0.0000010000,(CY068465_A_California_VRDL308_2009_2009/04/29:0.0000010000,CY068545_A_California_VRDL322_2009_2009/05/04:0.0000010000)100:0.0011599850)93:0.0005789299,(CY068726_A_California_VRDL196_2009_2009/04/29:0.0011573500,(CY072190_A_California_VRDL347_2009_2009/05/23:0.0000010000,CY068025_A_California_VRDL351_2009_2009/05/23:0.0000010000)97:0.0005791484)16:0.0000010000)16:0.0000010000)18:0.0000010000,(CY064855_A_California_VRDL144_2009_2009/04/27:0.0000010000,(CY068862_A_California_VRDL391_2009_2009/04/28:0.0000010000,CY067229_A_California_VRDL304_2009_2009/05/07:0.0000010000)68:0.0000010000)98:0.0005793989)44:0.0000010000,(((CY064823_A_California_VRDL138_2009_2009/04/27:0.0000010000,(CY068377_A_California_VRDL268_2009_2009/04/30:0.0000010000,CY068417_A_California_VRDL278_2009_2009/04/30:0.0000010000)31:0.0000010000)47:0.0000010000,CY068401_A_California_VRDL274_2009_2009/04/30:0.0000010000)63:0.0000010000,CY066519_A_California_VRDL156_2009_2009/04/28:0.0005789033)99:0.0023270677)91:0.0005788209,CY068609_A_California_VRDL335_2009_2009/05/03:0.0040861572)78:0.0005788208,CY068313_A_California_VRDL253_2009_2009/04/30:0.0070319180)34:0.0000010000,((CY068177_A_California_VRDL166_2009_2009/04/28:0.0005791927,CY068193_A_California_VRDL169_2009_2009/04/28:0.0000010000)98:0.0011589183,CY068449_A_California_VRDL294_2009_2009/04/30:0.0029082689)10:0.0000010000)9:0.0000010000,((CY068782_A_California_VRDL207_2009_2009/04/27:0.0052710469,CY067929_A_California_VRDL177_2009_2009/04/28:0.0017506015)88:0.0005706489,CY068097_A_California_VRDL368_2009_2009/04/27:0.0029090753)29:0.0000010000)24:0.0000010000)99:0.0017400824,CY092369_A_California_VRDL255_2009_2009/04/29:0.0000010000)97:0.0011606476,CY067953_A_California_VRDL288_2009_2009/04/30:0.0023269891)21:0.0000010000,CY068121_A_California_VRDL375_2009_2009/04/27:0.0005796556)12:0.0000010000,((CY068321_A_California_VRDL259_2009_2009/04/29:0.0029084788,CY068617_A_California_VRDL336_2009_2009/05/05:0.0029076239)48:0.0000010000,CY068433_A_California_VRDL285_2009_2009/04/30:0.0005794250)16:0.0000010000)4:0.0000010000,((((CY067921_A_California_VRDL176_2009_2009/04/27:0.0000010000,CY068041_A_California_VRDL354_2009_2009/05/26:0.0000010000)89:0.0000010000,((CY068822_A_California_VRDL381_2009_2009/04/27:0.0000010000,CY067237_A_California_VRDL307_2009_2009/05/02:0.0000010000)81:0.0000010000,CY068561_A_California_VRDL327_2009_2009/05/11:0.0005797302)99:0.0005789564)90:0.0005786560,CY068065_A_California_VRDL360_2009_2009/06/03:0.0011610138)92:0.0005794902,((CY068033_A_California_VRDL352_2009_2009/05/11:0.0000010000,CY068049_A_California_VRDL355_2009_2009/05/11:0.0000010000)97:0.0011595337,(CY068009_A_California_VRDL345_2009_2009/05/26:0.0000010000,CY068017_A_California_VRDL349_2009_2009/05/26:0.0000010000)100:0.0023254571)35:0.0000010000)8:0.0000010000)5:0.0000010000,(CY068129_A_California_VRDL396_2009_2009/04/28:0.0011642230,CY068585_A_California_VRDL332_2009_2009/05/11:0.0005797627)19:0.0000010000)19:0.0000010000,((((((CY068854_A_California_VRDL390_2009_2009/04/26:0.0005790711,CY068686_A_California_VRDL181_2009_2009/04/28:0.0011584859)42:0.0000010000,(CY068457_A_California_VRDL305_2009_2009/05/01:0.0000010000,CY067245_A_California_VRDL314_2009_2009/05/01:0.0000010000)99:0.0005791911)21:0.0000010000,((((((((((CY064863_A_California_VRDL145_2009_2009/04/27:0.0000010000,CY068105_A_California_VRDL373_2009_2009/04/27:0.0000010000)20:0.0000010000,(CY068169_A_California_VRDL165_2009_2009/04/29:0.0000010000,CY068329_A_California_VRDL260_2009_2009/05/01:0.0000010000)41:0.0000010000)2:0.0000010000,(CY068297_A_California_VRDL248_2009_2009/04/27:0.0000010000,CY068870_A_California_VRDL392_2009_2009/04/28:0.0000010000)17:0.0000010000)45:0.0000010000,(CY068497_A_California_VRDL313_2009_2009/05/01:0.0005789034,CY068505_A_California_VRDL315_2009_2009/05/01:0.0005788261)7:0.0000010000)99:0.0017389894,(CY068702_A_California_VRDL184_2009_2009/04/28:0.0000010000,CY068529_A_California_VRDL319_2009_2009/05/06:0.0000010000)99:0.0005789803)61:0.0000010000,((CY068742_A_California_VRDL199_2009_2009/04/28:0.0000010000,CY068569_A_California_VRDL329_2009_2009/05/09:0.0000010000)10:0.0000010000,CY068393_A_California_VRDL272_2009_2009/04/30:0.0000010000)50:0.0000010000)19:0.0000010000,(CY067977_A_California_VRDL340_2009_2009/05/04:0.0000010000,CY068513_A_California_VRDL317_2009_2009/05/06:0.0000010000)70:0.0000010000)95:0.0005789905,CY068353_A_California_VRDL263_2009_2009/04/30:0.0005787746)34:0.0000010000,CY068137_A_California_VRDL159_2009_2009/04/28:0.0000010000)21:0.0000010000,CY068577_A_California_VRDL331_2009_2009/05/11:0.0000010000)9:0.0000010000)3:0.0000010000,(CY068217_A_California_VRDL173_2009_2009/04/28:0.0000010000,CY068806_A_California_VRDL246_2009_2009/04/29:0.0000010000)34:0.0000010000)32:0.0000010000,CY067213_A_California_VRDL296_2009_2009/04/30:0.0005794845)91:0.0005784603,CY067969_A_California_VRDL339_2009_2009/05/04:0.0017411175)87:0.0005799012)87:0.0005789989,(CY092377_A_California_VRDL257_2009_2009/05/01:0.0017425393,CY068001_A_California_VRDL344_2009_2009/05/19:0.0005799059)25:0.0000010000)18:0.0000010000,CY068409_A_California_VRDL277_2009_2009/04/30:0.0000010000)14:0.0000010000,(((CY068766_A_California_VRDL204_2009_2009/04/28:0.0017432411,CY067993_A_California_VRDL343_2009_2009/05/11:0.0005797781)24:0.0000010000,CY067197_A_California_VRDL241_2009_2009/04/29:0.0000010000)10:0.0000010000,(((CY068718_A_California_VRDL187_2009_2009/04/28:0.0000010000,CY068265_A_California_VRDL231_2009_2009/04/30:0.0000010000)26:0.0000010000,CY089540_A_California_VRDL359_2009_2009/06/08:0.0005793607)15:0.0000010000,(CY068281_A_California_VRDL243_2009_2009/04/29:0.0005796586,(CY068521_A_California_VRDL318_2009_2009/05/06:0.0011579374,(CY067961_A_California_VRDL328_2009_2009/05/09:0.0000010000,CY070919_A_California_VRDL330_2009_2009/05/09:0.0000010000)97:0.0011597184)92:0.0005811200)12:0.0000010000)9:0.0000010000)14:0.0000010000)20:0.0000010000,(CY067945_A_California_VRDL287_2009_2009/05/04:0.0000010000,CY068057_A_California_VRDL357_2009_2009/06/05:0.0000010000)99:0.0005799001);
CONSENSUS TREE
--------------
Consensus tree is constructed from 1000 bootstrap trees
Log-likelihood of consensus tree: -4072.589248
Robinson-Foulds distance between ML tree and consensus tree: 50
Branches with support >0.000000% are kept (extended consensus)
Branch lengths are optimized by maximum likelihood on original alignment
Numbers in parentheses are bootstrap supports (%)
+-----CY068113_A_California_VRDL374_2009_2009/04/25
|
| +--CY068838_A_California_VRDL384_2009_2009/04/25
| +---------------| (100)
| | +--CY068625_A_California_VRDL338_2009_2009/05/18
| +-----| (97)
| | | +**CY072198_A_California_VRDL385_2009_2009/04/26
| | | +--|
| | | | +**CY068337_A_California_VRDL261_2009_2009/05/02
| | | +--| (8)
| | | | +--CY068710_A_California_VRDL185_2009_2009/04/29
| | | +--| (3)
| | | | | +--CY068846_A_California_VRDL387_2009_2009/04/27
| | | | | +-----| (97)
| | | | | | | +--CY068750_A_California_VRDL201_2009_2009/04/29
| | | | | | +--| (60)
| | | | | | +--CY068241_A_California_VRDL212_2009_2009/04/29
| | | | | +--| (23)
| | | | | | | +--CY068233_A_California_VRDL211_2009_2009/04/28
| | | | | | +-----| (98)
| | | | | | +--CY068537_A_California_VRDL321_2009_2009/05/04
| | | | +--| (14)
| | | | | +--CY068633_A_California_VRDL394_2009_2009/04/28
| | | | | +--| (24)
| | | | | | +--CY068734_A_California_VRDL198_2009_2009/04/28
| | | | | +--| (26)
| | | | | | +--CY068481_A_California_VRDL310_2009_2009/04/30
| | | | +--| (16)
| | | | | +**CY068153_A_California_VRDL161_2009_2009/04/28
| | | | | +--|
| | | | | | +**CY068225_A_California_VRDL188_2009_2009/04/29
| | | | +--| (21)
| | | | +--CY068185_A_California_VRDL168_2009_2009/04/29
| | | +--| (2)
| | | | +-----CY068774_A_California_VRDL205_2009_2009/04/29
| | | +--| (29)
| | | | | +-----CY068305_A_California_VRDL250_2009_2009/04/29
| | | | +--| (6)
| | | | | +**CY068814_A_California_VRDL269_2009_2009/04/30
| | | | +--|
| | | | +**CY068489_A_California_VRDL312_2009_2009/05/01
| | | +--| (96)
| | | | +--------CY068209_A_California_VRDL172_2009_2009/04/28
| | | +--| (24)
| | | | | +--CY068878_A_California_VRDL393_2009_2009/04/29
| | | | +-----| (99)
| | | | +--CY068385_A_California_VRDL271_2009_2009/04/30
| | | +--| (16)
| | | | | +**CY068678_A_California_VRDL178_2009_2009/04/28
| | | | | +--|
| | | | | | +**CY068553_A_California_VRDL325_2009_2009/05/03
| | | | | +--| (75)
| | | | | | +--CY068257_A_California_VRDL230_2009_2009/04/29
| | | | | +--| (63)
| | | | | | +--CY068790_A_California_VRDL208_2009_2009/04/29
| | | | +--| (96)
| | | | +--CY092361_A_California_VRDL242_2009_2009/04/29
| | | +--| (89)
| | | | | +--CY064879_A_California_VRDL147_2009_2009/04/28
| | | | +--| (20)
| | | | +--CY068289_A_California_VRDL247_2009_2009/04/29
| | +--| (92)
| | +-----CY067205_A_California_VRDL291_2009_2009/05/01
| +--| (91)
| | +---------------CY068758_A_California_VRDL203_2009_2009/04/28
| +--------| (99)
| | | +--CY064815_A_California_VRDL136_2009_2009/04/26
| | | +--| (87)
| | | | +--CY068161_A_California_VRDL164_2009_2009/04/28
| | | +------------------| (100)
| | | | +--CY067221_A_California_VRDL302_2009_2009/04/28
| | | +--| (65)
| | | | | +-----CY068145_A_California_VRDL160_2009_2009/04/28
| | | | +--| (92)
| | | | +-----CY068201_A_California_VRDL170_2009_2009/04/28
| | | +--| (94)
| | | | +--CY067937_A_California_VRDL286_2009_2009/04/30
| | | +--| (31)
| | | | | +--CY068249_A_California_VRDL216_2009_2009/04/28
| | | | +--| (98)
| | | | +--CY068473_A_California_VRDL309_2009_2009/05/02
| | | +--| (11)
| | | | +---------------CY068593_A_California_VRDL333_2009_2009/05/06
| | | +--| (1)
| | | | | +--CY068694_A_California_VRDL183_2009_2009/04/27
| | | | | +--| (96)
| | | | | | +--CY068425_A_California_VRDL279_2009_2009/04/30
| | | | +--| (21)
| | | | +---------------CY068441_A_California_VRDL293_2009_2009/04/30
| | | +--| (6)
| | | | | +--CY064847_A_California_VRDL143_2009_2009/04/27
| | | | +------------| (100)
| | | | +-----CY092329_A_California_VRDL182_2009_2009/04/28
| | | +--| (9)
| | | | +------------CY092353_A_California_VRDL197_2009_2009/04/29
| | | +--| (8)
| | | | | +--CY072206_A_California_VRDL386_2009_2009/04/26
| | | | | +--| (78)
| | | | | | +--------CY068273_A_California_VRDL233_2009_2009/04/29
| | | | | +--| (25)
| | | | | | | +--CY068798_A_California_VRDL210_2009_2009/04/28
| | | | | | +--------| (99)
| | | | | | +--CY068369_A_California_VRDL266_2009_2009/04/30
| | | | +--| (14)
| | | | +--CY064887_A_California_VRDL158_2009_2009/04/27
| | | +--| (18)
| | | | | +--CY068830_A_California_VRDL383_2009_2009/04/26
| | | | | +--| (99)
| | | | | | +--CY067985_A_California_VRDL342_2009_2009/05/20
| | | | | +--| (65)
| | | | | | +-----CY067253_A_California_VRDL316_2009_2009/05/04
| | | | | +--| (93)
| | | | | | | +--CY068465_A_California_VRDL308_2009_2009/04/29
| | | | | | +-----| (100)
| | | | | | +--CY068545_A_California_VRDL322_2009_2009/05/04
| | | | +--| (16)
| | | | | +-----CY068726_A_California_VRDL196_2009_2009/04/29
| | | | +--| (16)
| | | | | +--CY072190_A_California_VRDL347_2009_2009/05/23
| | | | +--| (97)
| | | | +--CY068025_A_California_VRDL351_2009_2009/05/23
| | | +--| (44)
| | | | | +--CY064855_A_California_VRDL144_2009_2009/04/27
| | | | +--| (98)
| | | | | +--CY068862_A_California_VRDL391_2009_2009/04/28
| | | | +--| (68)
| | | | +--CY067229_A_California_VRDL304_2009_2009/05/07
| | | +--| (91)
| | | | | +--CY064823_A_California_VRDL138_2009_2009/04/27
| | | | | +--| (47)
| | | | | | | +--CY068377_A_California_VRDL268_2009_2009/04/30
| | | | | | +--| (31)
| | | | | | +--CY068417_A_California_VRDL278_2009_2009/04/30
| | | | | +--| (63)
| | | | | | +--CY068401_A_California_VRDL274_2009_2009/04/30
| | | | +------------| (99)
| | | | +--CY066519_A_California_VRDL156_2009_2009/04/28
| | | +--| (78)
| | | | +----------------------CY068609_A_California_VRDL335_2009_2009/05/03
| | | +--| (34)
| | | | +---------------------------------------CY068313_A_California_VRDL253_2009_2009/04/30
| | | +--| (22)
| | | | +---------------CY068449_A_California_VRDL294_2009_2009/04/30
| | | +--| (13)
| | | | | +-----------------------------CY068782_A_California_VRDL207_2009_2009/04/27
| | | | | +--| (88)
| | | | | | +--------CY067929_A_California_VRDL177_2009_2009/04/28
| | | | +--| (29)
| | | | +---------------CY068097_A_California_VRDL368_2009_2009/04/27
| | +--| (24)
| | | +--CY068177_A_California_VRDL166_2009_2009/04/28
| | +-----| (98)
| | +--CY068193_A_California_VRDL169_2009_2009/04/28
| +-----| (97)
| | +--CY092369_A_California_VRDL255_2009_2009/04/29
| +--| (21)
| | +------------CY067953_A_California_VRDL288_2009_2009/04/30
| +--| (7)
| | | +---------------CY068321_A_California_VRDL259_2009_2009/04/29
| | | +--| (48)
| | | | +---------------CY068617_A_California_VRDL336_2009_2009/05/05
| | +--| (16)
| | +--CY068433_A_California_VRDL285_2009_2009/04/30
| +--| (2)
| | | +--CY067921_A_California_VRDL176_2009_2009/04/27
| | | +--| (89)
| | | | +--CY068041_A_California_VRDL354_2009_2009/05/26
| | | +--| (90)
| | | | | +--CY068822_A_California_VRDL381_2009_2009/04/27
| | | | | +--| (81)
| | | | | | +--CY067237_A_California_VRDL307_2009_2009/05/02
| | | | +--| (99)
| | | | +--CY068561_A_California_VRDL327_2009_2009/05/11
| | | +--| (92)
| | | | +-----CY068065_A_California_VRDL360_2009_2009/06/03
| | +--| (13)
| | +--CY068121_A_California_VRDL375_2009_2009/04/27
| +--| (5)
| | | +--CY068033_A_California_VRDL352_2009_2009/05/11
| | | +-----| (97)
| | | | +--CY068049_A_California_VRDL355_2009_2009/05/11
| | +--| (35)
| | | +--CY068009_A_California_VRDL345_2009_2009/05/26
| | +------------| (100)
| | +--CY068017_A_California_VRDL349_2009_2009/05/26
| +--| (19)
| | | +-----CY068129_A_California_VRDL396_2009_2009/04/28
| | +--| (19)
| | +--CY068585_A_California_VRDL332_2009_2009/05/11
| +--| (87)
| | | +--CY068854_A_California_VRDL390_2009_2009/04/26
| | | +--| (42)
| | | | +-----CY068686_A_California_VRDL181_2009_2009/04/28
| | | +--| (21)
| | | | | +--CY068457_A_California_VRDL305_2009_2009/05/01
| | | | +--| (99)
| | | | +--CY067245_A_California_VRDL314_2009_2009/05/01
| | | +--| (10)
| | | | | +--CY068217_A_California_VRDL173_2009_2009/04/28
| | | | +--| (34)
| | | | +--CY068806_A_California_VRDL246_2009_2009/04/29
| | | +--| (32)
| | | | | +--CY064863_A_California_VRDL145_2009_2009/04/27
| | | | | +--| (38)
| | | | | | +--CY068870_A_California_VRDL392_2009_2009/04/28
| | | | | +--| (31)
| | | | | | +--CY068105_A_California_VRDL373_2009_2009/04/27
| | | | | +--| (42)
| | | | | | +--CY068297_A_California_VRDL248_2009_2009/04/27
| | | | | +--| (45)
| | | | | | | +--CY068169_A_California_VRDL165_2009_2009/04/29
| | | | | | +--| (41)
| | | | | | +--CY068329_A_California_VRDL260_2009_2009/05/01
| | | | | +--| (76)
| | | | | | +--CY068497_A_California_VRDL313_2009_2009/05/01
| | | | | +--------| (99)
| | | | | | +--CY068505_A_California_VRDL315_2009_2009/05/01
| | | | | +--| (61)
| | | | | | | +--CY068702_A_California_VRDL184_2009_2009/04/28
| | | | | | +--| (99)
| | | | | | +--CY068529_A_California_VRDL319_2009_2009/05/06
| | | | | +--| (95)
| | | | | | | +--CY068742_A_California_VRDL199_2009_2009/04/28
| | | | | | | +--| (50)
| | | | | | | | | +**CY068393_A_California_VRDL272_2009_2009/04/30
| | | | | | | | | +--|
| | | | | | | | | | +**CY068601_A_California_VRDL334_2009_2009/05/18
| | | | | | | | +--| (55)
| | | | | | | | +--CY068569_A_California_VRDL329_2009_2009/05/09
| | | | | | +--| (30)
| | | | | | | +--CY067977_A_California_VRDL340_2009_2009/05/04
| | | | | | +--| (70)
| | | | | | +--CY068513_A_California_VRDL317_2009_2009/05/06
| | | | | +--| (34)
| | | | | | +--CY068353_A_California_VRDL263_2009_2009/04/30
| | | | | +--| (21)
| | | | | | +--CY068137_A_California_VRDL159_2009_2009/04/28
| | | | +--| (9)
| | | | +--CY068577_A_California_VRDL331_2009_2009/05/11
| | | +--| (91)
| | | | +--CY067213_A_California_VRDL296_2009_2009/04/30
| | +--| (87)
| | +--------CY067969_A_California_VRDL339_2009_2009/05/04
| +--| (18)
| | | +--------CY092377_A_California_VRDL257_2009_2009/05/01
| | +--| (25)
| | +--CY068001_A_California_VRDL344_2009_2009/05/19
| +--| (14)
| | +--CY068409_A_California_VRDL277_2009_2009/04/30
+--| (20)
| | +--------CY068766_A_California_VRDL204_2009_2009/04/28
| | +--| (24)
| | | +--CY067993_A_California_VRDL343_2009_2009/05/11
| | +--| (10)
| | | +--CY067197_A_California_VRDL241_2009_2009/04/29
| +--| (14)
| | +**CY068718_A_California_VRDL187_2009_2009/04/28
| | +--|
| | | +**CY077425_A_California_VRDL356_2009_2009/06/02
| | +--| (26)
| | | +--CY068265_A_California_VRDL231_2009_2009/04/30
| | +--| (15)
| | | +--CY089540_A_California_VRDL359_2009_2009/06/08
| +--| (9)
| | +--CY068281_A_California_VRDL243_2009_2009/04/29
| +--| (12)
| | +-----CY068521_A_California_VRDL318_2009_2009/05/06
| +--| (92)
| | +--CY067961_A_California_VRDL328_2009_2009/05/09
| +-----| (97)
| +--CY070919_A_California_VRDL330_2009_2009/05/09
|
| +--CY067945_A_California_VRDL287_2009_2009/05/04
+--| (99)
+--CY068057_A_California_VRDL357_2009_2009/06/05
Consensus tree in newick format:
(CY068113_A_California_VRDL374_2009_2009/04/25:0.0011574764,((((((((((((((CY068838_A_California_VRDL384_2009_2009/04/25:0.0000021259,CY068625_A_California_VRDL338_2009_2009/05/18:0.0005787289)100:0.0029231207,((((((((((CY072198_A_California_VRDL385_2009_2009/04/26:0.0000000000,CY068337_A_California_VRDL261_2009_2009/05/02:0.0000000000):0.0000021259,CY068710_A_California_VRDL185_2009_2009/04/29:0.0000021259)8:0.0000021259,(((CY068846_A_California_VRDL387_2009_2009/04/27:0.0005795652,(CY068750_A_California_VRDL201_2009_2009/04/29:0.0000021259,CY068241_A_California_VRDL212_2009_2009/04/29:0.0000021259)60:0.0000021259)97:0.0011604378,(CY068233_A_California_VRDL211_2009_2009/04/28:0.0000021259,CY068537_A_California_VRDL321_2009_2009/05/04:0.0000021259)98:0.0011584173)23:0.0000021259,(((CY068633_A_California_VRDL394_2009_2009/04/28:0.0000021259,CY068734_A_California_VRDL198_2009_2009/04/28:0.0000021259)24:0.0000021259,CY068481_A_California_VRDL310_2009_2009/04/30:0.0000021259)26:0.0000021259,((CY068153_A_California_VRDL161_2009_2009/04/28:0.0000000000,CY068225_A_California_VRDL188_2009_2009/04/29:0.0000000000):0.0000021259,CY068185_A_California_VRDL168_2009_2009/04/29:0.0000021259)21:0.0000021259)16:0.0000021259)14:0.0000021259)3:0.0000021259,CY068774_A_California_VRDL205_2009_2009/04/29:0.0011598111)2:0.0000021259,(CY068305_A_California_VRDL250_2009_2009/04/29:0.0011638265,(CY068814_A_California_VRDL269_2009_2009/04/30:0.0000000000,CY068489_A_California_VRDL312_2009_2009/05/01:0.0000000000):0.0000021259)6:0.0000021259)29:0.0000021259,CY068209_A_California_VRDL172_2009_2009/04/28:0.0017411048)96:0.0005783510,(CY068878_A_California_VRDL393_2009_2009/04/29:0.0000021259,CY068385_A_California_VRDL271_2009_2009/04/30:0.0000021259)99:0.0011593470)24:0.0000021259,((((CY068678_A_California_VRDL178_2009_2009/04/28:0.0000000000,CY068553_A_California_VRDL325_2009_2009/05/03:0.0000000000):0.0000021259,CY068257_A_California_VRDL230_2009_2009/04/29:0.0000021259)75:0.0000021259,CY068790_A_California_VRDL208_2009_2009/04/29:0.0000021259)63:0.0000021259,CY092361_A_California_VRDL242_2009_2009/04/29:0.0000021259)96:0.0005781518)16:0.0000021259,(CY064879_A_California_VRDL147_2009_2009/04/28:0.0005789166,CY068289_A_California_VRDL247_2009_2009/04/29:0.0005789529)20:0.0000021259)89:0.0005782788,CY067205_A_California_VRDL291_2009_2009/05/01:0.0011624466)92:0.0005767070)97:0.0011646046,CY068758_A_California_VRDL203_2009_2009/04/28:0.0029151142)91:0.0005805267,((((((((((((((((((CY064815_A_California_VRDL136_2009_2009/04/26:0.0000021259,CY068161_A_California_VRDL164_2009_2009/04/28:0.0000021259)87:0.0000021259,CY067221_A_California_VRDL302_2009_2009/04/28:0.0005827706)100:0.0034954155,(CY068145_A_California_VRDL160_2009_2009/04/28:0.0011598342,CY068201_A_California_VRDL170_2009_2009/04/28:0.0011640298)92:0.0005779544)65:0.0000021259,CY067937_A_California_VRDL286_2009_2009/04/30:0.0005814855)94:0.0005786590,(CY068249_A_California_VRDL216_2009_2009/04/28:0.0000021259,CY068473_A_California_VRDL309_2009_2009/05/02:0.0000021259)98:0.0005796457)31:0.0000021259,CY068593_A_California_VRDL333_2009_2009/05/06:0.0029147727)11:0.0000021259,((CY068694_A_California_VRDL183_2009_2009/04/27:0.0000021259,CY068425_A_California_VRDL279_2009_2009/04/30:0.0000021259)96:0.0005783733,CY068441_A_California_VRDL293_2009_2009/04/30:0.0029071576)21:0.0000021259)1:0.0000021259,(CY064847_A_California_VRDL143_2009_2009/04/27:0.0000021259,CY092329_A_California_VRDL182_2009_2009/04/28:0.0011616811)100:0.0023283978)6:0.0000021259,CY092353_A_California_VRDL197_2009_2009/04/29:0.0023242036)9:0.0000021259,(((CY072206_A_California_VRDL386_2009_2009/04/26:0.0000021259,CY068273_A_California_VRDL233_2009_2009/04/29:0.0017414950)78:0.0005790482,(CY068798_A_California_VRDL210_2009_2009/04/28:0.0000021259,CY068369_A_California_VRDL266_2009_2009/04/30:0.0005816083)99:0.0017396843)25:0.0000021259,CY064887_A_California_VRDL158_2009_2009/04/27:0.0000021259)14:0.0000021259)8:0.0000021259,((((CY068830_A_California_VRDL383_2009_2009/04/26:0.0000021259,CY067985_A_California_VRDL342_2009_2009/05/20:0.0005799876)99:0.0005788596,CY067253_A_California_VRDL316_2009_2009/05/04:0.0011585632)65:0.0000021259,(CY068465_A_California_VRDL308_2009_2009/04/29:0.0000021259,CY068545_A_California_VRDL322_2009_2009/05/04:0.0000021259)100:0.0011603674)93:0.0005786331,(CY068726_A_California_VRDL196_2009_2009/04/29:0.0011577513,(CY072190_A_California_VRDL347_2009_2009/05/23:0.0000021259,CY068025_A_California_VRDL351_2009_2009/05/23:0.0000021259)97:0.0005789172)16:0.0000021259)16:0.0000021259)18:0.0000021259,(CY064855_A_California_VRDL144_2009_2009/04/27:0.0000021259,(CY068862_A_California_VRDL391_2009_2009/04/28:0.0000021259,CY067229_A_California_VRDL304_2009_2009/05/07:0.0000021259)68:0.0000021259)98:0.0005791175)44:0.0000021259,(((CY064823_A_California_VRDL138_2009_2009/04/27:0.0000021259,(CY068377_A_California_VRDL268_2009_2009/04/30:0.0000021259,CY068417_A_California_VRDL278_2009_2009/04/30:0.0000021259)31:0.0000021259)47:0.0000021259,CY068401_A_California_VRDL274_2009_2009/04/30:0.0000021259)63:0.0000021259,CY066519_A_California_VRDL156_2009_2009/04/28:0.0005787384)99:0.0023277617)91:0.0005786870,CY068609_A_California_VRDL335_2009_2009/05/03:0.0040870590)78:0.0005791420,CY068313_A_California_VRDL253_2009_2009/04/30:0.0070334780)34:0.0000021259,CY068449_A_California_VRDL294_2009_2009/04/30:0.0029095595)22:0.0000021259,((CY068782_A_California_VRDL207_2009_2009/04/27:0.0052731365,CY067929_A_California_VRDL177_2009_2009/04/28:0.0017512685)88:0.0005710568,CY068097_A_California_VRDL368_2009_2009/04/27:0.0029102963)29:0.0000021259)13:0.0000021259,(CY068177_A_California_VRDL166_2009_2009/04/28:0.0005788746,CY068193_A_California_VRDL169_2009_2009/04/28:0.0000021259)98:0.0011589939)24:0.0000021259)99:0.0017405214,CY092369_A_California_VRDL255_2009_2009/04/29:0.0000021259)97:0.0011606269,CY067953_A_California_VRDL288_2009_2009/04/30:0.0023269181)21:0.0000021259,((CY068321_A_California_VRDL259_2009_2009/04/29:0.0029083753,CY068617_A_California_VRDL336_2009_2009/05/05:0.0029075233)48:0.0000021259,CY068433_A_California_VRDL285_2009_2009/04/30:0.0005787954)16:0.0000021259)7:0.0000021259,((((CY067921_A_California_VRDL176_2009_2009/04/27:0.0000021259,CY068041_A_California_VRDL354_2009_2009/05/26:0.0000021259)89:0.0000021259,((CY068822_A_California_VRDL381_2009_2009/04/27:0.0000021259,CY067237_A_California_VRDL307_2009_2009/05/02:0.0000021259)81:0.0000021259,CY068561_A_California_VRDL327_2009_2009/05/11:0.0005790571)99:0.0005784068)90:0.0005780127,CY068065_A_California_VRDL360_2009_2009/06/03:0.0011612735)92:0.0005796157,CY068121_A_California_VRDL375_2009_2009/04/27:0.0005788986)13:0.0000021259)2:0.0000021259,((CY068033_A_California_VRDL352_2009_2009/05/11:0.0000021259,CY068049_A_California_VRDL355_2009_2009/05/11:0.0000021259)97:0.0011594506,(CY068009_A_California_VRDL345_2009_2009/05/26:0.0000021259,CY068017_A_California_VRDL349_2009_2009/05/26:0.0000021259)100:0.0023253268)35:0.0000021259)5:0.0000021259,(CY068129_A_California_VRDL396_2009_2009/04/28:0.0011641430,CY068585_A_California_VRDL332_2009_2009/05/11:0.0005790781)19:0.0000021259)19:0.0000021259,((((((CY068854_A_California_VRDL390_2009_2009/04/26:0.0005784307,CY068686_A_California_VRDL181_2009_2009/04/28:0.0011583899)42:0.0000021259,(CY068457_A_California_VRDL305_2009_2009/05/01:0.0000021259,CY067245_A_California_VRDL314_2009_2009/05/01:0.0000021259)99:0.0005785119)21:0.0000021259,(CY068217_A_California_VRDL173_2009_2009/04/28:0.0000021259,CY068806_A_California_VRDL246_2009_2009/04/29:0.0000021259)34:0.0000021259)10:0.0000021259,(((((((((((CY064863_A_California_VRDL145_2009_2009/04/27:0.0000021259,CY068870_A_California_VRDL392_2009_2009/04/28:0.0000021259)38:0.0000021259,CY068105_A_California_VRDL373_2009_2009/04/27:0.0000021259)31:0.0000021259,CY068297_A_California_VRDL248_2009_2009/04/27:0.0000021259)42:0.0000021259,(CY068169_A_California_VRDL165_2009_2009/04/29:0.0000021259,CY068329_A_California_VRDL260_2009_2009/05/01:0.0000021259)41:0.0000021259)45:0.0000021259,CY068497_A_California_VRDL313_2009_2009/05/01:0.0005792674)76:0.0000021259,CY068505_A_California_VRDL315_2009_2009/05/01:0.0005783908)99:0.0017395410,(CY068702_A_California_VRDL184_2009_2009/04/28:0.0000021259,CY068529_A_California_VRDL319_2009_2009/05/06:0.0000021259)99:0.0005785850)61:0.0000021259,((CY068742_A_California_VRDL199_2009_2009/04/28:0.0000021259,((CY068393_A_California_VRDL272_2009_2009/04/30:0.0000000000,CY068601_A_California_VRDL334_2009_2009/05/18:0.0000000000):0.0000021259,CY068569_A_California_VRDL329_2009_2009/05/09:0.0000021259)55:0.0000021259)50:0.0000021259,(CY067977_A_California_VRDL340_2009_2009/05/04:0.0000021259,CY068513_A_California_VRDL317_2009_2009/05/06:0.0000021259)70:0.0000021259)30:0.0000021259)95:0.0005782842,CY068353_A_California_VRDL263_2009_2009/04/30:0.0005781955)34:0.0000021259,CY068137_A_California_VRDL159_2009_2009/04/28:0.0000021259)21:0.0000021259,CY068577_A_California_VRDL331_2009_2009/05/11:0.0000021259)9:0.0000021259)32:0.0000021259,CY067213_A_California_VRDL296_2009_2009/04/30:0.0005785979)91:0.0005775774,CY067969_A_California_VRDL339_2009_2009/05/04:0.0017414872)87:0.0005796913)87:0.0005792632,(CY092377_A_California_VRDL257_2009_2009/05/01:0.0017424188,CY068001_A_California_VRDL344_2009_2009/05/19:0.0005801616)25:0.0000021259)18:0.0000021259,CY068409_A_California_VRDL277_2009_2009/04/30:0.0000021259)14:0.0000021259,(((CY068766_A_California_VRDL204_2009_2009/04/28:0.0017431134,CY067993_A_California_VRDL343_2009_2009/05/11:0.0005798422)24:0.0000021259,CY067197_A_California_VRDL241_2009_2009/04/29:0.0000021259)10:0.0000021259,((((CY068718_A_California_VRDL187_2009_2009/04/28:0.0000000000,CY077425_A_California_VRDL356_2009_2009/06/02:0.0000000000):0.0000021259,CY068265_A_California_VRDL231_2009_2009/04/30:0.0000021259)26:0.0000021259,CY089540_A_California_VRDL359_2009_2009/06/08:0.0005794175)15:0.0000021259,(CY068281_A_California_VRDL243_2009_2009/04/29:0.0005788217,(CY068521_A_California_VRDL318_2009_2009/05/06:0.0011581736,(CY067961_A_California_VRDL328_2009_2009/05/09:0.0000021259,CY070919_A_California_VRDL330_2009_2009/05/09:0.0000021259)97:0.0011599545)92:0.0005808843)12:0.0000021259)9:0.0000021259)14:0.0000021259)20:0.0000021259,(CY067945_A_California_VRDL287_2009_2009/05/04:0.0000021259,CY068057_A_California_VRDL357_2009_2009/06/05:0.0000021259)99:0.0005800302);
TIME STAMP
----------
Date and time: Fri Nov 4 18:38:58 2022
Total CPU time used: 149.41319 seconds (0h:2m:29s)
Total wall-clock time used: 78.1381712 seconds (0h:1m:18s)
IQ-TREE multicore version 2.1.2 COVID-edition for Mac OS X 64-bit built Mar 30 2021
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams.
Host: 9350L-206723-M.local (SSE4.2, 64 GB RAM)
Command: iqtree2 -s results/aligned/expected-2.fasta -st DNA -pre results/tree/expected-2.fasta -nt AUTO -m HKY+G -bb 1000 -seed 847202098 -ntmax 2
Seed: 847202098 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Fri Nov 4 18:37:40 2022
Kernel: SSE2 - auto-detect threads (10 CPU cores detected)
Reading alignment file results/aligned/expected-2.fasta ... Fasta format detected
Alignment most likely contains DNA/RNA sequences
Alignment has 138 sequences with 1734 columns, 181 distinct patterns
81 parsimony-informative, 106 singleton sites, 1547 constant sites
Gap/Ambiguity Composition p-value
1 CY068113_A_California_VRDL374_2009_2009/04/25 0.00% passed 100.00%
2 CY068838_A_California_VRDL384_2009_2009/04/25 0.00% passed 99.92%
3 CY068854_A_California_VRDL390_2009_2009/04/26 0.17% passed 99.84%
4 CY064815_A_California_VRDL136_2009_2009/04/26 0.12% passed 99.69%
5 CY068830_A_California_VRDL383_2009_2009/04/26 0.00% passed 99.96%
6 CY072206_A_California_VRDL386_2009_2009/04/26 0.17% passed 99.99%
7 CY072198_A_California_VRDL385_2009_2009/04/26 0.00% passed 99.99%
8 CY068782_A_California_VRDL207_2009_2009/04/27 0.00% passed 99.94%
9 CY064863_A_California_VRDL145_2009_2009/04/27 0.17% passed 99.97%
10 CY068297_A_California_VRDL248_2009_2009/04/27 0.12% passed 99.98%
11 CY068105_A_California_VRDL373_2009_2009/04/27 0.12% passed 99.98%
12 CY067921_A_California_VRDL176_2009_2009/04/27 0.00% passed 99.98%
13 CY068822_A_California_VRDL381_2009_2009/04/27 0.17% passed 99.84%
14 CY068121_A_California_VRDL375_2009_2009/04/27 0.00% passed 99.97%
15 CY068097_A_California_VRDL368_2009_2009/04/27 0.12% passed 99.91%
16 CY064847_A_California_VRDL143_2009_2009/04/27 0.12% passed 99.74%
17 CY064823_A_California_VRDL138_2009_2009/04/27 0.12% passed 99.96%
18 CY064887_A_California_VRDL158_2009_2009/04/27 0.23% passed 100.00%
19 CY064855_A_California_VRDL144_2009_2009/04/27 0.12% passed 99.99%
20 CY068694_A_California_VRDL183_2009_2009/04/27 0.00% passed 99.96%
21 CY068846_A_California_VRDL387_2009_2009/04/27 0.17% passed 99.98%
22 CY068758_A_California_VRDL203_2009_2009/04/28 0.17% passed 99.77%
23 CY068870_A_California_VRDL392_2009_2009/04/28 0.17% passed 99.97%
24 CY068686_A_California_VRDL181_2009_2009/04/28 0.17% passed 99.95%
25 CY068702_A_California_VRDL184_2009_2009/04/28 0.12% passed 99.97%
26 CY068137_A_California_VRDL159_2009_2009/04/28 0.00% passed 99.98%
27 CY068217_A_California_VRDL173_2009_2009/04/28 0.17% passed 99.95%
28 CY068742_A_California_VRDL199_2009_2009/04/28 0.12% passed 99.98%
29 CY068129_A_California_VRDL396_2009_2009/04/28 0.63% passed 99.89%
30 CY068766_A_California_VRDL204_2009_2009/04/28 0.12% passed 99.84%
31 CY068718_A_California_VRDL187_2009_2009/04/28 0.17% passed 100.00%
32 CY068161_A_California_VRDL164_2009_2009/04/28 0.00% passed 99.51%
33 CY067221_A_California_VRDL302_2009_2009/04/28 0.69% passed 99.82%
34 CY067929_A_California_VRDL177_2009_2009/04/28 0.17% passed 99.75%
35 CY092329_A_California_VRDL182_2009_2009/04/28 0.12% passed 99.73%
36 CY068177_A_California_VRDL166_2009_2009/04/28 0.00% passed 99.98%
37 CY068193_A_California_VRDL169_2009_2009/04/28 0.17% passed 99.94%
38 CY066519_A_California_VRDL156_2009_2009/04/28 0.12% passed 99.97%
39 CY068145_A_California_VRDL160_2009_2009/04/28 0.00% passed 99.88%
40 CY068201_A_California_VRDL170_2009_2009/04/28 0.17% passed 99.93%
41 CY068798_A_California_VRDL210_2009_2009/04/28 0.00% passed 99.94%
42 CY068862_A_California_VRDL391_2009_2009/04/28 0.17% passed 99.98%
43 CY068249_A_California_VRDL216_2009_2009/04/28 0.17% passed 99.99%
44 CY068209_A_California_VRDL172_2009_2009/04/28 0.17% passed 99.82%
45 CY064879_A_California_VRDL147_2009_2009/04/28 0.17% passed 99.93%
46 CY068678_A_California_VRDL178_2009_2009/04/28 0.17% passed 99.99%
47 CY068233_A_California_VRDL211_2009_2009/04/28 0.00% passed 99.90%
48 CY068633_A_California_VRDL394_2009_2009/04/28 0.58% passed 99.98%
49 CY068734_A_California_VRDL198_2009_2009/04/28 0.40% passed 99.99%
50 CY068153_A_California_VRDL161_2009_2009/04/28 0.12% passed 99.99%
51 CY068321_A_California_VRDL259_2009_2009/04/29 0.17% passed 100.00%
52 CY068169_A_California_VRDL165_2009_2009/04/29 0.00% passed 99.95%
53 CY068806_A_California_VRDL246_2009_2009/04/29 0.17% passed 99.95%
54 CY092369_A_California_VRDL255_2009_2009/04/29 0.06% passed 99.98%
55 CY068281_A_California_VRDL243_2009_2009/04/29 0.17% passed 100.00%
56 CY067197_A_California_VRDL241_2009_2009/04/29 0.12% passed 99.99%
57 CY092353_A_California_VRDL197_2009_2009/04/29 0.00% passed 99.76%
58 CY068465_A_California_VRDL308_2009_2009/04/29 0.17% passed 99.90%
59 CY068273_A_California_VRDL233_2009_2009/04/29 0.12% passed 99.69%
60 CY068726_A_California_VRDL196_2009_2009/04/29 0.00% passed 99.88%
61 CY068878_A_California_VRDL393_2009_2009/04/29 0.17% passed 99.97%
62 CY068750_A_California_VRDL201_2009_2009/04/29 0.17% passed 99.97%
63 CY068241_A_California_VRDL212_2009_2009/04/29 0.06% passed 99.96%
64 CY068289_A_California_VRDL247_2009_2009/04/29 0.17% passed 99.93%
65 CY068305_A_California_VRDL250_2009_2009/04/29 0.58% passed 100.00%
66 CY068790_A_California_VRDL208_2009_2009/04/29 0.12% passed 100.00%
67 CY068257_A_California_VRDL230_2009_2009/04/29 0.17% passed 99.99%
68 CY092361_A_California_VRDL242_2009_2009/04/29 0.00% passed 99.99%
69 CY068774_A_California_VRDL205_2009_2009/04/29 0.00% passed 99.83%
70 CY068185_A_California_VRDL168_2009_2009/04/29 0.12% passed 99.99%
71 CY068710_A_California_VRDL185_2009_2009/04/29 0.00% passed 99.99%
72 CY068225_A_California_VRDL188_2009_2009/04/29 0.12% passed 99.99%
73 CY068313_A_California_VRDL253_2009_2009/04/30 0.17% passed 99.56%
74 CY067953_A_California_VRDL288_2009_2009/04/30 0.23% passed 99.97%
75 CY067213_A_California_VRDL296_2009_2009/04/30 0.17% passed 99.99%
76 CY068353_A_California_VRDL263_2009_2009/04/30 0.12% passed 99.85%
77 CY068393_A_California_VRDL272_2009_2009/04/30 0.17% passed 99.97%
78 CY068433_A_California_VRDL285_2009_2009/04/30 0.12% passed 100.00%
79 CY068265_A_California_VRDL231_2009_2009/04/30 0.17% passed 100.00%
80 CY068409_A_California_VRDL277_2009_2009/04/30 0.00% passed 99.96%
81 CY068449_A_California_VRDL294_2009_2009/04/30 0.17% passed 99.97%
82 CY068441_A_California_VRDL293_2009_2009/04/30 0.17% passed 99.99%
83 CY068377_A_California_VRDL268_2009_2009/04/30 0.12% passed 99.96%
84 CY068401_A_California_VRDL274_2009_2009/04/30 0.00% passed 99.90%
85 CY068417_A_California_VRDL278_2009_2009/04/30 0.17% passed 99.98%
86 CY068369_A_California_VRDL266_2009_2009/04/30 0.58% passed 99.96%
87 CY067937_A_California_VRDL286_2009_2009/04/30 0.58% passed 99.83%
88 CY068425_A_California_VRDL279_2009_2009/04/30 0.00% passed 99.96%
89 CY068385_A_California_VRDL271_2009_2009/04/30 0.17% passed 99.97%
90 CY068814_A_California_VRDL269_2009_2009/04/30 0.17% passed 99.96%
91 CY068481_A_California_VRDL310_2009_2009/04/30 0.17% passed 99.96%
92 CY068497_A_California_VRDL313_2009_2009/05/01 0.00% passed 99.97%
93 CY068505_A_California_VRDL315_2009_2009/05/01 0.00% passed 99.90%
94 CY068329_A_California_VRDL260_2009_2009/05/01 0.00% passed 99.95%
95 CY068457_A_California_VRDL305_2009_2009/05/01 0.17% passed 99.96%
96 CY067245_A_California_VRDL314_2009_2009/05/01 0.17% passed 99.96%
97 CY092377_A_California_VRDL257_2009_2009/05/01 0.12% passed 99.94%
98 CY067205_A_California_VRDL291_2009_2009/05/01 0.17% passed 99.95%
99 CY068489_A_California_VRDL312_2009_2009/05/01 0.17% passed 99.96%
100 CY067237_A_California_VRDL307_2009_2009/05/02 0.17% passed 99.84%
101 CY068473_A_California_VRDL309_2009_2009/05/02 0.17% passed 99.99%
102 CY068337_A_California_VRDL261_2009_2009/05/02 0.00% passed 99.99%
103 CY068609_A_California_VRDL335_2009_2009/05/03 0.17% passed 99.85%
104 CY068553_A_California_VRDL325_2009_2009/05/03 0.17% passed 99.99%
105 CY067969_A_California_VRDL339_2009_2009/05/04 0.12% passed 99.63%
106 CY067977_A_California_VRDL340_2009_2009/05/04 0.00% passed 99.98%
107 CY067945_A_California_VRDL287_2009_2009/05/04 0.17% passed 100.00%
108 CY068545_A_California_VRDL322_2009_2009/05/04 0.17% passed 99.90%
109 CY067253_A_California_VRDL316_2009_2009/05/04 0.00% passed 99.62%
110 CY068537_A_California_VRDL321_2009_2009/05/04 0.00% passed 99.90%
111 CY068617_A_California_VRDL336_2009_2009/05/05 0.17% passed 99.99%
112 CY068529_A_California_VRDL319_2009_2009/05/06 0.17% passed 99.93%
113 CY068513_A_California_VRDL317_2009_2009/05/06 0.00% passed 99.98%
114 CY068521_A_California_VRDL318_2009_2009/05/06 0.00% passed 99.80%
115 CY068593_A_California_VRDL333_2009_2009/05/06 0.17% passed 99.99%
116 CY067229_A_California_VRDL304_2009_2009/05/07 0.17% passed 99.98%
117 CY068569_A_California_VRDL329_2009_2009/05/09 0.17% passed 99.97%
118 CY067961_A_California_VRDL328_2009_2009/05/09 0.23% passed 99.93%
119 CY070919_A_California_VRDL330_2009_2009/05/09 0.17% passed 99.93%
120 CY068577_A_California_VRDL331_2009_2009/05/11 0.12% passed 99.96%
121 CY068561_A_California_VRDL327_2009_2009/05/11 0.17% passed 99.88%
122 CY068033_A_California_VRDL352_2009_2009/05/11 0.17% passed 99.98%
123 CY068049_A_California_VRDL355_2009_2009/05/11 0.17% passed 99.98%
124 CY068585_A_California_VRDL332_2009_2009/05/11 0.17% passed 99.99%
125 CY067993_A_California_VRDL343_2009_2009/05/11 0.17% passed 99.98%
126 CY068601_A_California_VRDL334_2009_2009/05/18 0.17% passed 99.97%
127 CY068625_A_California_VRDL338_2009_2009/05/18 0.17% passed 99.54%
128 CY068001_A_California_VRDL344_2009_2009/05/19 0.17% passed 100.00%
129 CY067985_A_California_VRDL342_2009_2009/05/20 0.17% passed 99.90%
130 CY072190_A_California_VRDL347_2009_2009/05/23 0.12% passed 99.97%
131 CY068025_A_California_VRDL351_2009_2009/05/23 0.17% passed 99.99%
132 CY068009_A_California_VRDL345_2009_2009/05/26 0.12% passed 99.66%
133 CY068017_A_California_VRDL349_2009_2009/05/26 0.12% passed 99.66%
134 CY068041_A_California_VRDL354_2009_2009/05/26 0.17% passed 99.95%
135 CY077425_A_California_VRDL356_2009_2009/06/02 0.17% passed 100.00%
136 CY068065_A_California_VRDL360_2009_2009/06/03 0.17% passed 99.99%
137 CY068057_A_California_VRDL357_2009_2009/06/05 0.17% passed 100.00%
138 CY089540_A_California_VRDL359_2009_2009/06/08 0.12% passed 99.99%
**** TOTAL 0.14% 0 sequences failed composition chi2 test (p-value<5%; df=3)
NOTE: CY068710_A_California_VRDL185_2009_2009/04/29 is identical to CY072198_A_California_VRDL385_2009_2009/04/26 but kept for subsequent analysis
NOTE: CY068870_A_California_VRDL392_2009_2009/04/28 is identical to CY064863_A_California_VRDL145_2009_2009/04/27 but kept for subsequent analysis
NOTE: CY068105_A_California_VRDL373_2009_2009/04/27 is identical to CY068297_A_California_VRDL248_2009_2009/04/27 but kept for subsequent analysis
NOTE: CY067237_A_California_VRDL307_2009_2009/05/02 is identical to CY068822_A_California_VRDL381_2009_2009/04/27 but kept for subsequent analysis
NOTE: CY068377_A_California_VRDL268_2009_2009/04/30 is identical to CY064823_A_California_VRDL138_2009_2009/04/27 but kept for subsequent analysis
NOTE: CY068425_A_California_VRDL279_2009_2009/04/30 is identical to CY068694_A_California_VRDL183_2009_2009/04/27 but kept for subsequent analysis
NOTE: CY068806_A_California_VRDL246_2009_2009/04/29 is identical to CY068217_A_California_VRDL173_2009_2009/04/28 but kept for subsequent analysis
NOTE: CY068265_A_California_VRDL231_2009_2009/04/30 is identical to CY068718_A_California_VRDL187_2009_2009/04/28 but kept for subsequent analysis
NOTE: CY067229_A_California_VRDL304_2009_2009/05/07 is identical to CY068862_A_California_VRDL391_2009_2009/04/28 but kept for subsequent analysis
NOTE: CY068473_A_California_VRDL309_2009_2009/05/02 is identical to CY068249_A_California_VRDL216_2009_2009/04/28 but kept for subsequent analysis
NOTE: CY068257_A_California_VRDL230_2009_2009/04/29 is identical to CY068678_A_California_VRDL178_2009_2009/04/28 but kept for subsequent analysis
NOTE: CY068537_A_California_VRDL321_2009_2009/05/04 is identical to CY068233_A_California_VRDL211_2009_2009/04/28 but kept for subsequent analysis
NOTE: CY068185_A_California_VRDL168_2009_2009/04/29 is identical to CY068153_A_California_VRDL161_2009_2009/04/28 but kept for subsequent analysis
NOTE: CY068329_A_California_VRDL260_2009_2009/05/01 is identical to CY068169_A_California_VRDL165_2009_2009/04/29 but kept for subsequent analysis
NOTE: CY068545_A_California_VRDL322_2009_2009/05/04 is identical to CY068465_A_California_VRDL308_2009_2009/04/29 but kept for subsequent analysis
NOTE: CY068385_A_California_VRDL271_2009_2009/04/30 is identical to CY068878_A_California_VRDL393_2009_2009/04/29 but kept for subsequent analysis
NOTE: CY068569_A_California_VRDL329_2009_2009/05/09 is identical to CY068393_A_California_VRDL272_2009_2009/04/30 but kept for subsequent analysis
NOTE: CY068481_A_California_VRDL310_2009_2009/04/30 is identical to CY068814_A_California_VRDL269_2009_2009/04/30 but kept for subsequent analysis
NOTE: CY067245_A_California_VRDL314_2009_2009/05/01 is identical to CY068457_A_California_VRDL305_2009_2009/05/01 but kept for subsequent analysis
NOTE: CY068513_A_California_VRDL317_2009_2009/05/06 is identical to CY067977_A_California_VRDL340_2009_2009/05/04 but kept for subsequent analysis
NOTE: CY068057_A_California_VRDL357_2009_2009/06/05 is identical to CY067945_A_California_VRDL287_2009_2009/05/04 but kept for subsequent analysis
NOTE: CY068049_A_California_VRDL355_2009_2009/05/11 is identical to CY068033_A_California_VRDL352_2009_2009/05/11 but kept for subsequent analysis
NOTE: CY068017_A_California_VRDL349_2009_2009/05/26 is identical to CY068009_A_California_VRDL345_2009_2009/05/26 but kept for subsequent analysis
NOTE: 6 identical sequences (see below) will be ignored for subsequent analysis
NOTE: CY068337_A_California_VRDL261_2009_2009/05/02 (identical to CY072198_A_California_VRDL385_2009_2009/04/26) is ignored but added at the end
NOTE: CY077425_A_California_VRDL356_2009_2009/06/02 (identical to CY068718_A_California_VRDL187_2009_2009/04/28) is ignored but added at the end
NOTE: CY068553_A_California_VRDL325_2009_2009/05/03 (identical to CY068678_A_California_VRDL178_2009_2009/04/28) is ignored but added at the end
NOTE: CY068225_A_California_VRDL188_2009_2009/04/29 (identical to CY068153_A_California_VRDL161_2009_2009/04/28) is ignored but added at the end
NOTE: CY068601_A_California_VRDL334_2009_2009/05/18 (identical to CY068393_A_California_VRDL272_2009_2009/04/30) is ignored but added at the end
NOTE: CY068489_A_California_VRDL312_2009_2009/05/01 (identical to CY068814_A_California_VRDL269_2009_2009/04/30) is ignored but added at the end
Alignment was printed to results/tree/expected-2.fasta.uniqueseq.phy
For your convenience alignment with unique sequences printed to results/tree/expected-2.fasta.uniqueseq.phy
Creating fast initial parsimony tree by random order stepwise addition...
0.045 seconds, parsimony score: 216 (based on 187 sites)
Generating 1000 samples for ultrafast bootstrap (seed: 847202098)...
NOTE: 3 MB RAM (0 GB) is required!
Measuring multi-threading efficiency up to 2 CPU cores
Increase to 10 rounds for branch lengths
51 trees examined
Threads: 1 / Time: 2.008 sec / Speedup: 1.000 / Efficiency: 100% / LogL: -7804
Threads: 2 / Time: 1.618 sec / Speedup: 1.240 / Efficiency: 62% / LogL: -7804
BEST NUMBER OF THREADS: 2
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -4195.306
2. Current log-likelihood: -4125.084
3. Current log-likelihood: -4124.979
4. Current log-likelihood: -4124.877
5. Current log-likelihood: -4124.775
6. Current log-likelihood: -4124.672
7. Current log-likelihood: -4124.569
8. Current log-likelihood: -4124.465
9. Current log-likelihood: -4124.360
10. Current log-likelihood: -4124.255
11. Current log-likelihood: -4124.149
12. Current log-likelihood: -4124.043
13. Current log-likelihood: -4123.936
14. Current log-likelihood: -4123.828
15. Current log-likelihood: -4123.720
16. Current log-likelihood: -4123.611
17. Current log-likelihood: -4123.502
18. Current log-likelihood: -4123.392
19. Current log-likelihood: -4123.281
20. Current log-likelihood: -4123.169
21. Current log-likelihood: -4123.057
22. Current log-likelihood: -4122.944
23. Current log-likelihood: -4122.831
24. Current log-likelihood: -4122.716
25. Current log-likelihood: -4122.601
26. Current log-likelihood: -4122.485
27. Current log-likelihood: -4122.369
28. Current log-likelihood: -4122.252
29. Current log-likelihood: -4122.134
30. Current log-likelihood: -4122.015
31. Current log-likelihood: -4121.896
32. Current log-likelihood: -4121.775
33. Current log-likelihood: -4121.654
34. Current log-likelihood: -4121.532
35. Current log-likelihood: -4121.410
36. Current log-likelihood: -4121.286
37. Current log-likelihood: -4121.162
38. Current log-likelihood: -4121.037
39. Current log-likelihood: -4120.910
40. Current log-likelihood: -4120.784
41. Current log-likelihood: -4120.656
42. Current log-likelihood: -4120.527
43. Current log-likelihood: -4120.397
44. Current log-likelihood: -4120.267
45. Current log-likelihood: -4120.135
46. Current log-likelihood: -4120.003
47. Current log-likelihood: -4119.870
48. Current log-likelihood: -4119.735
49. Current log-likelihood: -4119.600
50. Current log-likelihood: -4119.464
51. Current log-likelihood: -4119.326
52. Current log-likelihood: -4119.188
53. Current log-likelihood: -4119.049
54. Current log-likelihood: -4118.908
55. Current log-likelihood: -4118.767
56. Current log-likelihood: -4118.624
57. Current log-likelihood: -4118.480
58. Current log-likelihood: -4118.335
59. Current log-likelihood: -4118.189
60. Current log-likelihood: -4118.042
61. Current log-likelihood: -4117.894
62. Current log-likelihood: -4117.744
63. Current log-likelihood: -4117.594
64. Current log-likelihood: -4117.442
65. Current log-likelihood: -4117.288
66. Current log-likelihood: -4117.134
67. Current log-likelihood: -4116.978
68. Current log-likelihood: -4116.821
69. Current log-likelihood: -4116.662
70. Current log-likelihood: -4116.503
71. Current log-likelihood: -4116.341
72. Current log-likelihood: -4116.179
73. Current log-likelihood: -4116.015
74. Current log-likelihood: -4115.849
75. Current log-likelihood: -4115.682
76. Current log-likelihood: -4115.513
77. Current log-likelihood: -4115.343
78. Current log-likelihood: -4115.172
79. Current log-likelihood: -4114.998
80. Current log-likelihood: -4114.824
81. Current log-likelihood: -4114.647
82. Current log-likelihood: -4114.469
83. Current log-likelihood: -4114.289
84. Current log-likelihood: -4114.107
85. Current log-likelihood: -4113.924
86. Current log-likelihood: -4113.738
87. Current log-likelihood: -4113.551
88. Current log-likelihood: -4113.362
89. Current log-likelihood: -4113.171
90. Current log-likelihood: -4112.978
91. Current log-likelihood: -4112.783
92. Current log-likelihood: -4112.586
93. Current log-likelihood: -4112.387
94. Current log-likelihood: -4112.186
95. Current log-likelihood: -4111.983
96. Current log-likelihood: -4111.777
97. Current log-likelihood: -4111.569
98. Current log-likelihood: -4111.359
99. Current log-likelihood: -4111.147
Optimal log-likelihood: -4111.147
Rate parameters: A-C: 1.00000 A-G: 63.19886 A-T: 1.00000 C-G: 1.00000 C-T: 63.19886 G-T: 1.00000
Base frequencies: A: 0.341 C: 0.199 G: 0.218 T: 0.242
Gamma shape alpha: 0.424
Parameters optimization took 99 rounds (1.045 sec)
Computing ML distances based on estimated model parameters...
Computing ML distances took 0.044004 sec (of wall-clock time) 0.087908 sec(of CPU time)
Computing RapidNJ tree took 0.001465 sec (of wall-clock time) 0.004164 sec (of CPU time)
Log-likelihood of RapidNJ tree: -4112.735
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.747 second
Computing log-likelihood of 98 initial trees ... 0.310 seconds
Current best score: -4105.549
Do NNI search on 20 best initial trees
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -4072.274
BETTER TREE FOUND at iteration 2: -4072.274
Iteration 10 / LogL: -4072.274 / Time: 0h:0m:7s
BETTER TREE FOUND at iteration 13: -4072.274
BETTER TREE FOUND at iteration 19: -4072.274
Iteration 20 / LogL: -4072.274 / Time: 0h:0m:7s
Finish initializing candidate tree set (20)
Current best tree score: -4072.274 / CPU time: 2.913
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Iteration 30 / LogL: -4077.496 / Time: 0h:0m:9s (0h:0m:27s left)
Iteration 40 / LogL: -4090.396 / Time: 0h:0m:10s (0h:0m:21s left)
Iteration 50 / LogL: -4072.310 / Time: 0h:0m:12s (0h:0m:16s left)
Log-likelihood cutoff on original alignment: -4123.694
Iteration 60 / LogL: -4076.174 / Time: 0h:0m:13s (0h:0m:13s left)
Iteration 70 / LogL: -4104.646 / Time: 0h:0m:15s (0h:0m:10s left)
Iteration 80 / LogL: -4072.313 / Time: 0h:0m:16s (0h:0m:8s left)
Iteration 90 / LogL: -4120.092 / Time: 0h:0m:17s (0h:0m:5s left)
Iteration 100 / LogL: -4072.301 / Time: 0h:0m:19s (0h:0m:3s left)
Log-likelihood cutoff on original alignment: -4123.694
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.978
NOTE: UFBoot does not converge, continue at least 100 more iterations
Iteration 110 / LogL: -4077.571 / Time: 0h:0m:21s (0h:0m:17s left)
Iteration 120 / LogL: -4077.667 / Time: 0h:0m:23s (0h:0m:15s left)
Iteration 130 / LogL: -4072.308 / Time: 0h:0m:24s (0h:0m:13s left)
Iteration 140 / LogL: -4077.921 / Time: 0h:0m:26s (0h:0m:11s left)
Iteration 150 / LogL: -4084.438 / Time: 0h:0m:27s (0h:0m:9s left)
Log-likelihood cutoff on original alignment: -4123.688
Iteration 160 / LogL: -4082.933 / Time: 0h:0m:29s (0h:0m:7s left)
Iteration 170 / LogL: -4074.771 / Time: 0h:0m:31s (0h:0m:5s left)
Iteration 180 / LogL: -4091.935 / Time: 0h:0m:32s (0h:0m:3s left)
Iteration 190 / LogL: -4075.925 / Time: 0h:0m:34s (0h:0m:1s left)
Iteration 200 / LogL: -4072.305 / Time: 0h:0m:36s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -4123.688
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.988
NOTE: UFBoot does not converge, continue at least 100 more iterations
Iteration 210 / LogL: -4072.327 / Time: 0h:0m:38s (0h:0m:16s left)
Iteration 220 / LogL: -4072.333 / Time: 0h:0m:40s (0h:0m:14s left)
Iteration 230 / LogL: -4072.321 / Time: 0h:0m:42s (0h:0m:13s left)
Iteration 240 / LogL: -4072.318 / Time: 0h:0m:44s (0h:0m:11s left)
Iteration 250 / LogL: -4092.899 / Time: 0h:0m:46s (0h:0m:9s left)
Log-likelihood cutoff on original alignment: -4123.688
Iteration 260 / LogL: -4072.315 / Time: 0h:0m:48s (0h:0m:7s left)
Iteration 270 / LogL: -4077.677 / Time: 0h:0m:50s (0h:0m:5s left)
Iteration 280 / LogL: -4072.326 / Time: 0h:0m:52s (0h:0m:3s left)
Iteration 290 / LogL: -4072.292 / Time: 0h:0m:54s (0h:0m:1s left)
Iteration 300 / LogL: -4072.322 / Time: 0h:0m:56s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -4123.688
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.989
NOTE: UFBoot does not converge, continue at least 100 more iterations
Iteration 310 / LogL: -4085.174 / Time: 0h:0m:58s (0h:0m:17s left)
Iteration 320 / LogL: -4072.323 / Time: 0h:1m:0s (0h:0m:15s left)
Iteration 330 / LogL: -4080.354 / Time: 0h:1m:2s (0h:0m:13s left)
Iteration 340 / LogL: -4072.314 / Time: 0h:1m:4s (0h:0m:11s left)
Iteration 350 / LogL: -4087.203 / Time: 0h:1m:6s (0h:0m:9s left)
Log-likelihood cutoff on original alignment: -4123.688
Iteration 360 / LogL: -4072.317 / Time: 0h:1m:8s (0h:0m:7s left)
Iteration 370 / LogL: -4076.173 / Time: 0h:1m:10s (0h:0m:5s left)
Iteration 380 / LogL: -4072.337 / Time: 0h:1m:13s (0h:0m:3s left)
Iteration 390 / LogL: -4076.987 / Time: 0h:1m:15s (0h:0m:1s left)
Iteration 400 / LogL: -4075.876 / Time: 0h:1m:17s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -4124.060
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.994
TREE SEARCH COMPLETED AFTER 400 ITERATIONS / Time: 0h:1m:17s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -4072.274
Optimal log-likelihood: -4072.274
Rate parameters: A-C: 1.00000 A-G: 10.16464 A-T: 1.00000 C-G: 1.00000 C-T: 10.16464 G-T: 1.00000
Base frequencies: A: 0.341 C: 0.199 G: 0.218 T: 0.242
Gamma shape alpha: 0.438
Parameters optimization took 1 rounds (0.008 sec)
BEST SCORE FOUND : -4072.274
Creating bootstrap support values...
Split supports printed to NEXUS file results/tree/expected-2.fasta.splits.nex
Total tree length: 0.126
Total number of iterations: 400
CPU time used for tree search: 142.703 sec (0h:2m:22s)
Wall-clock time used for tree search: 72.877 sec (0h:1m:12s)
Total CPU time used: 149.413 sec (0h:2m:29s)
Total wall-clock time used: 78.016 sec (0h:1m:18s)
Computing bootstrap consensus tree...
Reading input file results/tree/expected-2.fasta.splits.nex...
132 taxa and 3815 splits.
Consensus tree written to results/tree/expected-2.fasta.contree
Reading input trees file results/tree/expected-2.fasta.contree
Log-likelihood of consensus tree: -4072.589
Analysis results written to:
IQ-TREE report: results/tree/expected-2.fasta.iqtree
Maximum-likelihood tree: results/tree/expected-2.fasta.treefile
Likelihood distances: results/tree/expected-2.fasta.mldist
Ultrafast bootstrap approximation results written to:
Split support values: results/tree/expected-2.fasta.splits.nex
Consensus tree: results/tree/expected-2.fasta.contree
Screen log file: results/tree/expected-2.fasta.log
Date and Time: Fri Nov 4 18:38:58 2022
Quality Control
Beast
| None | mean | sd | hdi_3% | hdi_97% | mcse_mean | mcse_sd | ess_bulk | ess_tail | r_hat |
|---|---|---|---|---|---|---|---|---|---|
| posterior | -6252.216 | 437.294 | -7101.322 | -5768.224 | 162.691 | 120.033 | 7.0 | 7.0 | — |
| likelihood | -5482.223 | 403.334 | -6273.078 | -5038.021 | 150.056 | 110.711 | 7.0 | 7.0 | — |
| prior | -769.993 | 34.93 | -828.244 | -725.043 | 12.995 | 9.588 | 7.0 | 7.0 | — |
| treeLikelihood | -5482.223 | 403.334 | -6273.078 | -5038.021 | 150.056 | 110.711 | 7.0 | 7.0 | — |
| TreeHeight | 12.35 | 3.135 | 7.824 | 16.528 | 1.166 | 0.86 | 7.0 | 7.0 | — |
| kappa | 6.314 | 0.286 | 6.188 | 7.075 | 0.106 | 0.078 | 7.0 | 7.0 | — |
| gammaShape | 0.235 | 0.024 | 0.196 | 0.269 | 0.009 | 0.006 | 7.0 | 7.0 | — |
| CoalescentExponential | -753.374 | 34.696 | -811.176 | -708.847 | 12.908 | 9.524 | 7.0 | 7.0 | — |
| ePopSize | 538.885 | 133.929 | 364.59 | 816.848 | 49.827 | 36.762 | 7.0 | 7.0 | — |
| growthRate | 0.49 | 0.152 | 0.29 | 0.754 | 0.057 | 0.042 | 7.0 | 7.0 | — |
| freqParameter1 | 0.329 | 0.022 | 0.301 | 0.359 | 0.008 | 0.006 | 7.0 | 7.0 | — |
| freqParameter2 | 0.199 | 0.007 | 0.196 | 0.217 | 0.003 | 0.002 | 7.0 | 7.0 | — |
| freqParameter3 | 0.226 | 0.008 | 0.215 | 0.236 | 0.003 | 0.002 | 7.0 | 7.0 | — |
| freqParameter4 | 0.246 | 0.012 | 0.23 | 0.259 | 0.004 | 0.003 | 7.0 | 7.0 | — |
<?xml version="1.0" ?><beast beautitemplate="Standard" beautistatus="" namespace="beast.core:beast.evolution.alignment:feast:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood" required="" version="2.6">
<alignment id="alignment" spec="feast.fileio.AlignmentFromFasta" fileName="$(alignment)"/>
<map name="Uniform">beast.math.distributions.Uniform</map>
<map name="Exponential">beast.math.distributions.Exponential</map>
<map name="LogNormal">beast.math.distributions.LogNormalDistributionModel</map>
<map name="Normal">beast.math.distributions.Normal</map>
<map name="Beta">beast.math.distributions.Beta</map>
<map name="Gamma">beast.math.distributions.Gamma</map>
<map name="LaplaceDistribution">beast.math.distributions.LaplaceDistribution</map>
<map name="prior">beast.math.distributions.Prior</map>
<map name="InverseGamma">beast.math.distributions.InverseGamma</map>
<map name="OneOnX">beast.math.distributions.OneOnX</map>
<run id="mcmc" spec="$(mcmc.spec=MCMC)" chainLength="$(mcmc.chainLength=100000000)">
<state id="state" spec="$(state.spec=State)" storeEvery="$(state.storeEvery=5000)">
<tree id="Tree" spec="$(Tree.spec=beast.evolution.tree.Tree)" name="$(Tree.name=stateNode)">
<trait id="Date" spec="$(Date.spec=feast.fileio.TraitSetFromTaxonSet)" delimiter="$(Date.delimiter=|)" everythingAfterLast="$(Date.everythingAfterLast=true)" dateFormat="$(Date.dateFormat=Y)" traitname="$(Date.traitname=date)">
<taxa id="taxonSet" spec="$(taxonSet.spec=TaxonSet)" alignment="$(taxonSet.alignment=@alignment)"/>
</trait>
<taxonset idref="taxonSet"/>
</tree>
<parameter id="kappa" spec="$(kappa.spec=parameter.RealParameter)" lower="$(kappa.lower=0.0)" name="$(kappa.name=stateNode)">$(kappa=2.0)</parameter>
<parameter id="gammaShape" spec="$(gammaShape.spec=parameter.RealParameter)" name="$(gammaShape.name=stateNode)">$(gammaShape=1.0)</parameter>
<parameter id="ePopSize" spec="$(ePopSize.spec=parameter.RealParameter)" name="$(ePopSize.name=stateNode)">$(ePopSize=0.3)</parameter>
<parameter id="growthRate" spec="$(growthRate.spec=parameter.RealParameter)" name="$(growthRate.name=stateNode)">$(growthRate=3.0E-4)</parameter>
<parameter id="freqParameter" spec="$(freqParameter.spec=parameter.RealParameter)" dimension="$(freqParameter.dimension=4)" lower="$(freqParameter.lower=0.0)" name="$(freqParameter.name=stateNode)" upper="$(freqParameter.upper=1.0)">$(freqParameter=0.25)</parameter>
</state>
<init id="RandomTree" spec="$(RandomTree.spec=beast.evolution.tree.RandomTree)" estimate="$(RandomTree.estimate=false)" initial="$(RandomTree.initial=@Tree)" taxa="$(RandomTree.taxa=@alignment)">
<populationModel id="ConstantPopulation0" spec="$(ConstantPopulation0.spec=ConstantPopulation)">
<parameter id="randomPopSize" spec="$(randomPopSize.spec=parameter.RealParameter)" name="$(randomPopSize.name=popSize)">$(randomPopSize=1.0)</parameter>
</populationModel>
</init>
<distribution id="posterior" spec="$(posterior.spec=util.CompoundDistribution)">
<distribution id="prior" spec="$(prior.spec=util.CompoundDistribution)">
<distribution id="CoalescentExponential" spec="$(CoalescentExponential.spec=Coalescent)">
<populationModel id="ExponentialGrowth" spec="$(ExponentialGrowth.spec=ExponentialGrowth)" growthRate="$(ExponentialGrowth.growthRate=@growthRate)" popSize="$(ExponentialGrowth.popSize=@ePopSize)"/>
<treeIntervals id="TreeIntervals" spec="$(TreeIntervals.spec=TreeIntervals)" tree="$(TreeIntervals.tree=@Tree)"/>
</distribution>
<prior id="ePopSizePrior" name="$(ePopSizePrior.name=distribution)" x="$(ePopSizePrior.x=@ePopSize)">
<OneOnX id="OneOnX.1" name="$(OneOnX.1.name=distr)"/>
</prior>
<prior id="FrequenciesPrior" name="$(FrequenciesPrior.name=distribution)" x="$(FrequenciesPrior.x=@freqParameter)">
<Uniform id="Uniform.3" name="$(Uniform.3.name=distr)"/>
</prior>
<prior id="GammaShapePrior" name="$(GammaShapePrior.name=distribution)" x="$(GammaShapePrior.x=@gammaShape)">
<Exponential id="Exponential.0" name="$(Exponential.0.name=distr)">
<parameter id="RealParameter.0" spec="$(RealParameter.0.spec=parameter.RealParameter)" estimate="$(RealParameter.0.estimate=false)" name="$(RealParameter.0.name=mean)">$(RealParameter.0=1.0)</parameter>
</Exponential>
</prior>
<prior id="GrowthRatePrior" name="$(GrowthRatePrior.name=distribution)" x="$(GrowthRatePrior.x=@growthRate)">
<LaplaceDistribution id="LaplaceDistribution.0" name="$(LaplaceDistribution.0.name=distr)">
<parameter id="RealParameter.3" spec="$(RealParameter.3.spec=parameter.RealParameter)" estimate="$(RealParameter.3.estimate=false)" name="$(RealParameter.3.name=mu)">$(RealParameter.3=0.0)</parameter>
<parameter id="RealParameter.4" spec="$(RealParameter.4.spec=parameter.RealParameter)" estimate="$(RealParameter.4.estimate=false)" name="$(RealParameter.4.name=scale)">$(RealParameter.4=500.0)</parameter>
</LaplaceDistribution>
</prior>
<prior id="KappaPrior" name="$(KappaPrior.name=distribution)" x="$(KappaPrior.x=@kappa)">
<LogNormal id="LogNormalDistributionModel.0" name="$(LogNormalDistributionModel.0.name=distr)">
<parameter id="RealParameter.1" spec="$(RealParameter.1.spec=parameter.RealParameter)" estimate="$(RealParameter.1.estimate=false)" name="$(RealParameter.1.name=M)">$(RealParameter.1=1.0)</parameter>
<parameter id="RealParameter.2" spec="$(RealParameter.2.spec=parameter.RealParameter)" estimate="$(RealParameter.2.estimate=false)" name="$(RealParameter.2.name=S)">$(RealParameter.2=1.25)</parameter>
</LogNormal>
</prior>
</distribution>
<distribution id="likelihood" spec="$(likelihood.spec=util.CompoundDistribution)" useThreads="$(likelihood.useThreads=true)">
<distribution id="treeLikelihood" spec="$(treeLikelihood.spec=ThreadedTreeLikelihood)" data="$(treeLikelihood.data=@alignment)" tree="$(treeLikelihood.tree=@Tree)">
<siteModel id="SiteModel" spec="$(SiteModel.spec=SiteModel)" gammaCategoryCount="$(SiteModel.gammaCategoryCount=4)" shape="$(SiteModel.shape=@gammaShape)">
<parameter id="mutationRate" spec="$(mutationRate.spec=parameter.RealParameter)" estimate="$(mutationRate.estimate=false)" name="$(mutationRate.name=mutationRate)">$(mutationRate=1.0)</parameter>
<parameter id="proportionInvariant" spec="$(proportionInvariant.spec=parameter.RealParameter)" estimate="$(proportionInvariant.estimate=false)" lower="$(proportionInvariant.lower=0.0)" name="$(proportionInvariant.name=proportionInvariant)" upper="$(proportionInvariant.upper=1.0)">$(proportionInvariant=0.0)</parameter>
<substModel id="hky" spec="$(hky.spec=HKY)" kappa="$(hky.kappa=@kappa)">
<frequencies id="estimatedFreqs" spec="$(estimatedFreqs.spec=Frequencies)" frequencies="$(estimatedFreqs.frequencies=@freqParameter)"/>
</substModel>
</siteModel>
<branchRateModel id="StrictClock.c" spec="$(StrictClock.c.spec=beast.evolution.branchratemodel.StrictClockModel)">
<parameter id="clockRate.c" spec="$(clockRate.c.spec=parameter.RealParameter)" estimate="$(clockRate.c.estimate=false)" name="$(clockRate.c.name=clock.rate)">$(clockRate.c=7.0E-4)</parameter>
</branchRateModel>
</distribution>
</distribution>
</distribution>
<operator id="KappaScaler" spec="$(KappaScaler.spec=ScaleOperator)" parameter="$(KappaScaler.parameter=@kappa)" scaleFactor="$(KappaScaler.scaleFactor=0.5)" weight="$(KappaScaler.weight=0.1)"/>
<operator id="gammaShapeScaler" spec="$(gammaShapeScaler.spec=ScaleOperator)" parameter="$(gammaShapeScaler.parameter=@gammaShape)" scaleFactor="$(gammaShapeScaler.scaleFactor=0.5)" weight="$(gammaShapeScaler.weight=0.1)"/>
<operator id="CoalescentExponentialTreeScaler" spec="$(CoalescentExponentialTreeScaler.spec=ScaleOperator)" scaleFactor="$(CoalescentExponentialTreeScaler.scaleFactor=0.5)" tree="$(CoalescentExponentialTreeScaler.tree=@Tree)" weight="$(CoalescentExponentialTreeScaler.weight=3.0)"/>
<operator id="CoalescentExponentialTreeRootScaler" spec="$(CoalescentExponentialTreeRootScaler.spec=ScaleOperator)" rootOnly="$(CoalescentExponentialTreeRootScaler.rootOnly=true)" scaleFactor="$(CoalescentExponentialTreeRootScaler.scaleFactor=0.5)" tree="$(CoalescentExponentialTreeRootScaler.tree=@Tree)" weight="$(CoalescentExponentialTreeRootScaler.weight=3.0)"/>
<operator id="CoalescentExponentialUniformOperator" spec="$(CoalescentExponentialUniformOperator.spec=Uniform)" tree="$(CoalescentExponentialUniformOperator.tree=@Tree)" weight="$(CoalescentExponentialUniformOperator.weight=30.0)"/>
<operator id="CoalescentExponentialSubtreeSlide" spec="$(CoalescentExponentialSubtreeSlide.spec=SubtreeSlide)" tree="$(CoalescentExponentialSubtreeSlide.tree=@Tree)" weight="$(CoalescentExponentialSubtreeSlide.weight=15.0)"/>
<operator id="CoalescentExponentialNarrow" spec="$(CoalescentExponentialNarrow.spec=Exchange)" tree="$(CoalescentExponentialNarrow.tree=@Tree)" weight="$(CoalescentExponentialNarrow.weight=15.0)"/>
<operator id="CoalescentExponentialWide" spec="$(CoalescentExponentialWide.spec=Exchange)" isNarrow="$(CoalescentExponentialWide.isNarrow=false)" tree="$(CoalescentExponentialWide.tree=@Tree)" weight="$(CoalescentExponentialWide.weight=3.0)"/>
<operator id="CoalescentExponentialWilsonBalding" spec="$(CoalescentExponentialWilsonBalding.spec=WilsonBalding)" tree="$(CoalescentExponentialWilsonBalding.tree=@Tree)" weight="$(CoalescentExponentialWilsonBalding.weight=3.0)"/>
<operator id="ePopSizeScaler" spec="$(ePopSizeScaler.spec=ScaleOperator)" parameter="$(ePopSizeScaler.parameter=@ePopSize)" weight="$(ePopSizeScaler.weight=3.0)"/>
<operator id="GrowthRateRandomWalk" spec="$(GrowthRateRandomWalk.spec=RealRandomWalkOperator)" parameter="$(GrowthRateRandomWalk.parameter=@growthRate)" weight="$(GrowthRateRandomWalk.weight=3.0)" windowSize="$(GrowthRateRandomWalk.windowSize=1.0)"/>
<operator id="FrequenciesExchanger" spec="$(FrequenciesExchanger.spec=DeltaExchangeOperator)" delta="$(FrequenciesExchanger.delta=0.01)" weight="$(FrequenciesExchanger.weight=0.1)">
<parameter idref="freqParameter"/>
</operator>
<logger id="tracelog" spec="$(tracelog.spec=Logger)" fileName="$(tracelog)" logEvery="$(tracelog.logEvery=10000)" model="$(tracelog.model=@posterior)" sanitiseHeaders="$(tracelog.sanitiseHeaders=true)" sort="$(tracelog.sort=smart)">
<log idref="posterior"/>
<log idref="likelihood"/>
<log idref="prior"/>
<log idref="treeLikelihood"/>
<log id="TreeHeight" spec="$(TreeHeight.spec=beast.evolution.tree.TreeHeightLogger)" tree="$(TreeHeight.tree=@Tree)"/>
<log idref="kappa"/>
<log idref="gammaShape"/>
<log idref="CoalescentExponential"/>
<log idref="ePopSize"/>
<log idref="growthRate"/>
<log idref="freqParameter"/>
</logger>
<logger id="screenlog" spec="$(screenlog.spec=Logger)" logEvery="$(screenlog.logEvery=1000)">
<log idref="posterior"/>
<log idref="likelihood"/>
<log idref="prior"/>
</logger>
<logger id="treelog" spec="$(treelog.spec=Logger)" fileName="$(treelog)" logEvery="$(treelog.logEvery=10000)" mode="$(treelog.mode=tree)">
<log id="TreeWithMetaDataLogger" spec="$(TreeWithMetaDataLogger.spec=beast.evolution.tree.TreeWithMetaDataLogger)" tree="$(TreeWithMetaDataLogger.tree=@Tree)"/>
</logger>
<operatorschedule id="OperatorSchedule" spec="$(OperatorSchedule.spec=OperatorSchedule)"/>
</run>
</beast>
Bibliography
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- Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler, Bui Quang Minh, and Le Sy Vinh. UFBoot2: Improving the Ultrafast Bootstrap Approximation. Molecular Biology and Evolution, 35(2):518–522, 10 2017. URL: https://doi.org/10.1093/molbev/msx281, arXiv:https://academic.oup.com/mbe/article-pdf/35/2/518/24367824/msx281.pdf, doi:10.1093/molbev/msx281.
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- Bui Quang Minh, Heiko A Schmidt, Olga Chernomor, Dominik Schrempf, Michael D Woodhams, Arndt von Haeseler, and Robert Lanfear. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Molecular Biology and Evolution, 37(5):1530–1534, 02 2020. URL: https://doi.org/10.1093/molbev/msaa015, arXiv:https://academic.oup.com/mbe/article-pdf/37/5/1530/33386032/msaa015.pdf, doi:10.1093/molbev/msaa015.
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- Remco Bouckaert, Timothy G. Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, Mathieu Fourment, Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kühnert, Nicola De Maio, Michael Matschiner, Fábio K. Mendes, Nicola F. Müller, Huw A. Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, David Rasmussen, Igor Siveroni, Marc A. Suchard, Chieh-Hsi Wu, Dong Xie, Chi Zhang, Tanja Stadler, and Alexei J. Drummond. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLOS Computational Biology, 15(4):1–28, April 2019. Publisher: Public Library of Science. URL: https://doi.org/10.1371/journal.pcbi.1006650, doi:10.1371/journal.pcbi.1006650.
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- Kazutaka Katoh and Daron M. Standley. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Molecular Biology and Evolution, 30(4):772–780, 01 2013. URL: https://doi.org/10.1093/molbev/mst010, arXiv:https://academic.oup.com/mbe/article-pdf/30/4/772/6420419/mst010.pdf, doi:10.1093/molbev/mst010.
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@article{eaton_toytree_2020,
author = "Eaton, Deren A. R.",
title = "Toytree: {A} minimalist tree visualization and manipulation library for {Python}",
volume = "11",
doi = "10.1111/2041-210X.13313",
journal = "Methods in Ecology and Evolution",
year = "2020",
pages = "187--191"
}
@article{10.1093/molbev/msx281,
author = "Hoang, Diep Thi and Chernomor, Olga and von Haeseler, Arndt and Minh, Bui Quang and Vinh, Le Sy",
title = "{UFBoot2: Improving the Ultrafast Bootstrap Approximation}",
journal = "Molecular Biology and Evolution",
volume = "35",
number = "2",
pages = "518-522",
year = "2017",
month = "10",
abstract = "{The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches. Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested data sets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.}",
issn = "0737-4038",
doi = "10.1093/molbev/msx281",
url = "https://doi.org/10.1093/molbev/msx281",
eprint = "https://academic.oup.com/mbe/article-pdf/35/2/518/24367824/msx281.pdf"
}
@article{10.1093/molbev/msaa015,
author = "Minh, Bui Quang and Schmidt, Heiko A and Chernomor, Olga and Schrempf, Dominik and Woodhams, Michael D and von Haeseler, Arndt and Lanfear, Robert",
title = "{IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era}",
journal = "Molecular Biology and Evolution",
volume = "37",
number = "5",
pages = "1530-1534",
year = "2020",
month = "02",
abstract = "{IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.}",
issn = "0737-4038",
doi = "10.1093/molbev/msaa015",
url = "https://doi.org/10.1093/molbev/msaa015",
eprint = "https://academic.oup.com/mbe/article-pdf/37/5/1530/33386032/msaa015.pdf"
}
@article{10.1371/journal.pcbi.1006650,
title = {{BEAST} 2.5: {An} advanced software platform for {Bayesian} evolutionary analysis},
volume = {15},
url = {https://doi.org/10.1371/journal.pcbi.1006650},
doi = {10.1371/journal.pcbi.1006650},
abstract = {Author summary Bayesian phylogenetic inference methods have undergone considerable development in recent years, and joint modelling of rich evolutionary data, including genomes, phenotypes and fossil occurrences is increasingly common. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing scientific software is increasingly crucial to advancement in many fields of biology. The challenges range from practical software development and engineering, distributed team coordination, conceptual development and statistical modelling, to validation and testing. BEAST 2 is one such computational software platform for phylogenetics, population genetics and phylodynamics, and was first announced over 4 years ago. Here we describe the full range of new tools and models available on the BEAST 2.5 platform, which expand joint evolutionary inference in many new directions, especially for joint inference over multiple data types, non-tree models and complex phylodynamics.},
number = {4},
journal = {PLOS Computational Biology},
author = {Bouckaert, Remco and Vaughan, Timothy G. and Barido-Sottani, Joëlle and Duchêne, Sebastián and Fourment, Mathieu and Gavryushkina, Alexandra and Heled, Joseph and Jones, Graham and Kühnert, Denise and De Maio, Nicola and Matschiner, Michael and Mendes, Fábio K. and Müller, Nicola F. and Ogilvie, Huw A. and du Plessis, Louis and Popinga, Alex and Rambaut, Andrew and Rasmussen, David and Siveroni, Igor and Suchard, Marc A. and Wu, Chieh-Hsi and Xie, Dong and Zhang, Chi and Stadler, Tanja and Drummond, Alexei J.},
month = apr,
year = {2019},
note = {Publisher: Public Library of Science},
pages = {1--28},
}
@article{10.1093/molbev/mst010,
author = {Katoh, Kazutaka and Standley, Daron M.},
title = "{MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability}",
journal = {Molecular Biology and Evolution},
volume = {30},
number = {4},
pages = {772-780},
year = {2013},
month = {01},
abstract = "{We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.}",
issn = {0737-4038},
doi = {10.1093/molbev/mst010},
url = {https://doi.org/10.1093/molbev/mst010},
eprint = {https://academic.oup.com/mbe/article-pdf/30/4/772/6420419/mst010.pdf},
}
@misc{wytamma_wirth_2022_7036457,
author = {Wytamma Wirth},
title = {Dynamic BEAST},
month = aug,
year = 2022,
publisher = {Zenodo},
version = {1.8.2},
doi = {10.5281/zenodo.7036457},
url = {https://doi.org/10.5281/zenodo.7036457}
}
@misc{feast,
author = {Tim Vaughan},
title = {feast: Tasty additions to BEAST 2},
year = 2022,
publisher = {GitHub},
url = {https://github.com/tgvaughan/feast}
}
@article{10.1093/bioinformatics/btab096,
author = {Steenwyk, Jacob L and Buida, Thomas J, III and Labella, Abigail L and Li, Yuanning and Shen, Xing-Xing and Rokas, Antonis},
title = "{PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data}",
journal = {Bioinformatics},
volume = {37},
number = {16},
pages = {2325-2331},
year = {2021},
month = {02},
abstract = "{Diverse disciplines in biology process and analyze multiple sequence alignments (MSAs) and phylogenetic trees to evaluate their information content, infer evolutionary events and processes and predict gene function. However, automated processing of MSAs and trees remains a challenge due to the lack of a unified toolkit. To fill this gap, we introduce PhyKIT, a toolkit for the UNIX shell environment with 30 functions that process MSAs and trees, including but not limited to estimation of mutation rate, evaluation of sequence composition biases, calculation of the degree of violation of a molecular clock and collapsing bipartitions (internal branches) with low support.To demonstrate the utility of PhyKIT, we detail three use cases: (1) summarizing information content in MSAs and phylogenetic trees for diagnosing potential biases in sequence or tree data; (2) evaluating gene–gene covariation of evolutionary rates to identify functional relationships, including novel ones, among genes and (3) identify lack of resolution events or polytomies in phylogenetic trees, which are suggestive of rapid radiation events or lack of data. We anticipate PhyKIT will be useful for processing, examining and deriving biological meaning from increasingly large phylogenomic datasets.PhyKIT is freely available on GitHub (https://github.com/JLSteenwyk/PhyKIT), PyPi (https://pypi.org/project/phykit/) and the Anaconda Cloud (https://anaconda.org/JLSteenwyk/phykit) under the MIT license with extensive documentation and user tutorials (https://jlsteenwyk.com/PhyKIT).Supplementary data are available at Bioinformatics online.}",
issn = {1367-4803},
doi = {10.1093/bioinformatics/btab096},
url = {https://doi.org/10.1093/bioinformatics/btab096},
eprint = {https://academic.oup.com/bioinformatics/article-pdf/37/16/2325/39948152/btab096.pdf},
}
@article{Steenwyk_2021,
doi = {10.1101/2021.10.02.462868},
url = {https://doi.org/10.1101%2F2021.10.02.462868},
year = 2021,
month = {oct},
journal = {biorxiv},
publisher = {Cold Spring Harbor Laboratory},
author = {Steenwyk, Jacob L. and Buida, Thomas J. and Gon{\c{c}}alves, Carla and Goltz, Dayna C. and Morales, Grace and Mead, Matthew E. and LaBella, Abigail L. and Chavez, Christina M. and Schmitz, Jonathan E. and Hadjifrangiskou, Maria and Li, Yuanning and Rokas, Antonis},
title = {{BioKIT}: a versatile toolkit for processing and analyzing diverse types of sequence data}
}